From 5ad584c0c4335c2e9e6cde54d011a3b09c114f63 Mon Sep 17 00:00:00 2001 From: oerc0042 Date: Mon, 10 Nov 2025 12:22:41 +0000 Subject: [PATCH] jupyter notebook testing and revisions/corrections --- ...e Sample Name field in assay tablets.ipynb | 14 +- ...ne Sample Name field in assay tables.ipynb | 237 +- ...Tab and back to ISA-json - roundtrip.ipynb | 202 +- ...treatment-design-with-ISA-descriptor.ipynb | 340 +- ...te-a-simple-ISA-descriptor-test-json.ipynb | 642 +- .../create-a-simple-ISA-descriptor.ipynb | 8 +- .../create_2x2x2_factorial_design.ipynb | 100 +- .../notebooks/create_ISA_sample_pools.ipynb | 882 +- ...tascriptor-crossover-study-on-humans.ipynb | 6 +- ...al-variables-and-ontology-annotation.ipynb | 9 +- .../isa-api-comprehensive-examples.ipynb | 979 + .../notebooks/isa-api-getting-started.ipynb | 530 + ...i-programmatic-BH2023-multiomics-isa.ipynb | 11 +- ...i-programmatic-BH2024-multiomics-isa.ipynb | 2 +- ...a-json-conversion-to-rdf-linked-data.ipynb | 6 +- .../isa-jsonld-exploration-with-SPARQL.ipynb | 6 +- ...isa-metabolomics-study-design-create.ipynb | 13650 +------------- ...l-type-synonym-effect-on-assay-table.ipynb | 1826 +- ...ign-4-arms-blood-derma-nmr-ms-chipseq.json | 3007 +-- ...-unused-sources-not-serialized-brapi.ipynb | 299 +- .../isa_template/a_assay_genotype.txt | 11 + .../isa_template/a_assay_metabolomics_OA.txt | 11 + .../a_assay_metabolomics_amines.txt | 11 + .../a_assay_metabolomics_steroids.txt | 11 + .../isa_template/a_assay_methylation.txt | 11 + .../isa_template/i_investigation.txt | 101 + .../notebooks/isa_template/s_study.txt | 21 + .../notebooks/json/BII-S-3/BII-S-3.json | 120 +- ...tity-study-repeated-treatment-design.ipynb | 1749 +- .../output/BII-S-9/a_gilbert-assay-Gx.txt | 5 - .../output/BII-S-9/i_investigation.txt | 99 - .../output/BII-S-9/s_BII-S-9-synthesic.txt | 5 - .../a_isotopologue-ms-assay.txt | 9 - .../a_isotopomer-nmr-assay.txt | 33 - .../a_metabolite-profiling-nmr-assay.txt | 9 - .../MTBLS-XXXX-SIRM/i_investigation.txt | 99 - .../output/MTBLS-XXXX-SIRM/isa-sirm-test.json | 4292 ----- .../MTBLS-XXXX-SIRM/s_13C-SIRM-study.txt | 9 - ...atic-rebuild-of-BII-S-3-with-ISA-API.ipynb | 6 +- ...querying-isa-with-graphql-and-sparql.ipynb | 53 +- ...b-from-disk-exploring-and-validating.ipynb | 29 +- isa-cookbook/content/notebooks/xomics.ipynb | 15570 ++-------------- 42 files changed, 6478 insertions(+), 38542 deletions(-) create mode 100644 isa-cookbook/content/notebooks/isa-api-comprehensive-examples.ipynb create mode 100644 isa-cookbook/content/notebooks/isa-api-getting-started.ipynb create mode 100644 isa-cookbook/content/notebooks/isa_template/a_assay_genotype.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_OA.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_amines.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_steroids.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/a_assay_methylation.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/i_investigation.txt create mode 100644 isa-cookbook/content/notebooks/isa_template/s_study.txt delete mode 100644 isa-cookbook/content/notebooks/output/BII-S-9/a_gilbert-assay-Gx.txt delete mode 100644 isa-cookbook/content/notebooks/output/BII-S-9/i_investigation.txt delete mode 100644 isa-cookbook/content/notebooks/output/BII-S-9/s_BII-S-9-synthesic.txt delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_isotopologue-ms-assay.txt delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_isotopomer-nmr-assay.txt delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_metabolite-profiling-nmr-assay.txt delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/i_investigation.txt delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/isa-sirm-test.json delete mode 100644 isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/s_13C-SIRM-study.txt diff --git a/isa-cookbook/content/notebooks/ISA-API - testing more than one Sample Name field in assay tablets.ipynb b/isa-cookbook/content/notebooks/ISA-API - testing more than one Sample Name field in assay tablets.ipynb index 777fd07c4..232e8253c 100644 --- a/isa-cookbook/content/notebooks/ISA-API - testing more than one Sample Name field in assay tablets.ipynb +++ b/isa-cookbook/content/notebooks/ISA-API - testing more than one Sample Name field in assay tablets.ipynb @@ -320,21 +320,13 @@ "# note the use of the flag for explicit serialization on factor values on assay tables\n", "dump(investigation, \"./output/BII-S-9/\", write_factor_values_in_assay_table=True)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "c1d38d02", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -346,7 +338,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/ISA-API -More than one Sample Name field in assay tables.ipynb b/isa-cookbook/content/notebooks/ISA-API -More than one Sample Name field in assay tables.ipynb index 68d616c4b..e7560079a 100644 --- a/isa-cookbook/content/notebooks/ISA-API -More than one Sample Name field in assay tables.ipynb +++ b/isa-cookbook/content/notebooks/ISA-API -More than one Sample Name field in assay tables.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 139, + "execution_count": null, "id": "30b2e3f5", "metadata": {}, "outputs": [], @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 140, + "execution_count": null, "id": "c71f1007", "metadata": {}, "outputs": [], @@ -190,7 +190,7 @@ }, { "cell_type": "code", - "execution_count": 141, + "execution_count": null, "id": "7ad0a00e", "metadata": {}, "outputs": [], @@ -228,7 +228,7 @@ }, { "cell_type": "code", - "execution_count": 142, + "execution_count": null, "id": "0b5c311f", "metadata": {}, "outputs": [], @@ -241,45 +241,10 @@ }, { "cell_type": "code", - "execution_count": 143, + "execution_count": null, "id": "cbabfc33", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Sample(\n", - " name=aliquot-0\n", - " characteristics=1 Characteristic objects\n", - " factor_values=0 FactorValue objects\n", - " derives_from=1 Source objects\n", - " comments=0 Comment objects\n", - ")\n", - "Sample(\n", - " name=aliquot-1\n", - " characteristics=1 Characteristic objects\n", - " factor_values=0 FactorValue objects\n", - " derives_from=1 Source objects\n", - " comments=0 Comment objects\n", - ")\n", - "Sample(\n", - " name=aliquot-2\n", - " characteristics=1 Characteristic objects\n", - " factor_values=0 FactorValue objects\n", - " derives_from=1 Source objects\n", - " comments=0 Comment objects\n", - ")\n", - "Sample(\n", - " name=aliquot-3\n", - " characteristics=1 Characteristic objects\n", - " factor_values=0 FactorValue objects\n", - " derives_from=1 Source objects\n", - " comments=0 Comment objects\n", - ")\n" - ] - } - ], + "outputs": [], "source": [ "# aliquots = [Sample(name=\"GSM255770.a1\"), Sample(name=\"GSM255771.a1\"), Sample(name=\"GSM255772.a1\"), Sample(name=\"GSM255773.a1\")] \n", "\n", @@ -355,24 +320,10 @@ }, { "cell_type": "code", - "execution_count": 144, + "execution_count": null, "id": "0bfa14cf", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Sample(\n", - " name=aliquot-3\n", - " characteristics=1 Characteristic objects\n", - " factor_values=0 FactorValue objects\n", - " derives_from=1 Source objects\n", - " comments=0 Comment objects\n", - ")\n" - ] - } - ], + "outputs": [], "source": [ "study.assays.append(assay)\n", "\n", @@ -384,172 +335,10 @@ }, { "cell_type": "code", - "execution_count": 146, + "execution_count": null, "id": "6736f5ff", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-08-02 18:39:47,234 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [616, 617, 618, 619]\n", - "2021-08-02 18:39:47,237 [WARNING]: isatab.py(write_study_table_files:1194) >> [624, 620, 616, 625, 621, 617, 626, 622, 618, 627, 623, 619]\n", - "2021-08-02 18:39:47,238 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[616, 624, 620], [617, 625, 621], [618, 626, 622], [619, 627, 623]]\n", - "2021-08-02 18:39:47,281 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [629, 620, 635, 621, 641, 622, 647, 623]\n", - "2021-08-02 18:39:47,282 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[629, 630, 631, 632], [629, 630], [620, 628, 629, 630], [620, 628, 629, 630, 631, 632], [635, 636], [635, 636, 637, 638], [621, 634, 635, 636], [621, 634, 635, 636, 637, 638], [641, 642], [641, 642, 643, 644], [622, 640, 641, 642], [622, 640, 641, 642, 643, 644], [647, 648], [647, 648, 649, 650], [623, 646, 647, 648], [623, 646, 647, 648, 649, 650]]\n", - "2021-08-02 18:39:47,282 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[629, 630, 631, 632], [629, 630], [620, 628, 629, 630], [620, 628, 629, 630, 631, 632], [635, 636], [635, 636, 637, 638], [621, 634, 635, 636], [621, 634, 635, 636, 637, 638], [641, 642], [641, 642, 643, 644], [622, 640, 641, 642], [622, 640, 641, 642, 643, 644], [647, 648], [647, 648, 649, 650], [623, 646, 647, 648], [623, 646, 647, 648, 649, 650]]\n", - "2021-08-02 18:39:47,297 [CRITICAL]: isatab.py(write_assay_table_files:1554) >> Error thrown: column labels are: Index(['Sample Name', 'Protocol REF.aliquoting-procedure', 'Sample Name',\n", - " 'Protocol REF.aliquoting-procedure', 'Extract Name',\n", - " 'Extract Name.Characteristics[Material Type]',\n", - " 'Extract Name.Characteristics[Material Type].Term Source REF',\n", - " 'Extract Name.Characteristics[Material Type].Term Accession Number',\n", - " 'Protocol REF.nucleic acid sequencing', 'Assay Name', 'Raw Data File',\n", - " 'Raw Data File.Comment[data_comment]'],\n", - " dtype='object')\n", - "2021-08-02 18:39:47,306 [CRITICAL]: isatab.py(write_assay_table_files:1555) >> Error thrown: data is: Sample Name Protocol REF.aliquoting-procedure Sample Name \\\n", - "0 aliquot-0 aliquoting-procedure aliquot-0 \n", - "1 aliquot-0 aliquoting-procedure aliquot-0 \n", - "2 aliquot-0 aliquoting-procedure aliquot-0 \n", - "3 aliquot-0 aliquoting-procedure aliquot-0 \n", - "4 aliquot-1 aliquoting-procedure aliquot-1 \n", - "5 aliquot-1 aliquoting-procedure aliquot-1 \n", - "6 aliquot-1 aliquoting-procedure aliquot-1 \n", - "7 aliquot-1 aliquoting-procedure aliquot-1 \n", - "8 aliquot-2 aliquoting-procedure aliquot-2 \n", - "9 aliquot-2 aliquoting-procedure aliquot-2 \n", - "10 aliquot-2 aliquoting-procedure aliquot-2 \n", - "11 aliquot-2 aliquoting-procedure aliquot-2 \n", - "12 aliquot-3 aliquoting-procedure aliquot-3 \n", - "13 aliquot-3 aliquoting-procedure aliquot-3 \n", - "14 aliquot-3 aliquoting-procedure aliquot-3 \n", - "15 aliquot-3 aliquoting-procedure aliquot-3 \n", - "\n", - " Protocol REF.aliquoting-procedure Extract Name \\\n", - "0 aliquoting-procedure extract-0 \n", - "1 aliquoting-procedure \n", - "2 aliquoting-procedure \n", - "3 aliquoting-procedure extract-0 \n", - "4 aliquoting-procedure \n", - "5 aliquoting-procedure extract-1 \n", - "6 aliquoting-procedure \n", - "7 aliquoting-procedure extract-1 \n", - "8 aliquoting-procedure \n", - "9 aliquoting-procedure extract-2 \n", - "10 aliquoting-procedure \n", - "11 aliquoting-procedure extract-2 \n", - "12 aliquoting-procedure \n", - "13 aliquoting-procedure extract-3 \n", - "14 aliquoting-procedure \n", - "15 aliquoting-procedure extract-3 \n", - "\n", - " Extract Name.Characteristics[Material Type] \\\n", - "0 pellet \n", - "1 \n", - "2 \n", - "3 pellet \n", - "4 \n", - "5 pellet \n", - "6 \n", - "7 pellet \n", - "8 \n", - "9 pellet \n", - "10 \n", - "11 pellet \n", - "12 \n", - "13 pellet \n", - "14 \n", - "15 pellet \n", - "\n", - " Extract Name.Characteristics[Material Type].Term Source REF \\\n", - "0 \n", - "1 \n", - "2 \n", - "3 \n", - "4 \n", - "5 \n", - "6 \n", - "7 \n", - "8 \n", - "9 \n", - "10 \n", - "11 \n", - "12 \n", - "13 \n", - "14 \n", - "15 \n", - "\n", - " Extract Name.Characteristics[Material Type].Term Accession Number \\\n", - "0 \n", - "1 \n", - "2 \n", - "3 \n", - "4 \n", - "5 \n", - "6 \n", - "7 \n", - "8 \n", - "9 \n", - "10 \n", - "11 \n", - "12 \n", - "13 \n", - "14 \n", - "15 \n", - "\n", - " Protocol REF.nucleic acid sequencing Assay Name Raw Data File \\\n", - "0 nucleic acid sequencing assay-name-0 sequenced-data-0 \n", - "1 \n", - "2 \n", - "3 nucleic acid sequencing assay-name-0 sequenced-data-0 \n", - "4 \n", - "5 nucleic acid sequencing assay-name-1 sequenced-data-1 \n", - "6 \n", - "7 nucleic acid sequencing assay-name-1 sequenced-data-1 \n", - "8 \n", - "9 nucleic acid sequencing assay-name-2 sequenced-data-2 \n", - "10 \n", - "11 nucleic acid sequencing assay-name-2 sequenced-data-2 \n", - "12 \n", - "13 nucleic acid sequencing assay-name-3 sequenced-data-3 \n", - "14 \n", - "15 nucleic acid sequencing assay-name-3 sequenced-data-3 \n", - "\n", - " Raw Data File.Comment[data_comment] \n", - "0 data_value \n", - "1 \n", - "2 \n", - "3 data_value \n", - "4 \n", - "5 data_value \n", - "6 \n", - "7 data_value \n", - "8 \n", - "9 data_value \n", - "10 \n", - "11 data_value \n", - "12 \n", - "13 data_value \n", - "14 \n", - "15 data_value \n" - ] - }, - { - "ename": "ValueError", - "evalue": "The column label 'Sample Name' is not unique.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/ipykernel_71489/407357070.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;31m# note the use of the flag for explicit serialization on factor values on assay tables\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mdump\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"./output/BII-S-10/\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mwrite_factor_values_in_assay_table\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mdump\u001b[0;34m(isa_obj, output_path, i_file_name, skip_dump_tables, write_factor_values_in_assay_table)\u001b[0m\n\u001b[1;32m 1048\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1049\u001b[0m \u001b[0mwrite_study_table_files\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1050\u001b[0;31m write_assay_table_files(\n\u001b[0m\u001b[1;32m 1051\u001b[0m investigation, output_path, write_factor_values_in_assay_table)\n\u001b[1;32m 1052\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_assay_table_files\u001b[0;34m(inv_obj, output_dir, write_factor_values)\u001b[0m\n\u001b[1;32m 1554\u001b[0m \u001b[0mlog\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcritical\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Error thrown: column labels are: {}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDF\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1555\u001b[0m \u001b[0mlog\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcritical\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Error thrown: data is: {}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDF\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1556\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1557\u001b[0m \u001b[0;31m# arbitrary sort on column 0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1558\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_assay_table_files\u001b[0;34m(inv_obj, output_dir, write_factor_values)\u001b[0m\n\u001b[1;32m 1550\u001b[0m \u001b[0mDF\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mDF\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;31m# reorder columns\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1551\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1552\u001b[0;31m \u001b[0mDF\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mDF\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msort_values\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mby\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mDF\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mascending\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1553\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mValueError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1554\u001b[0m \u001b[0mlog\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcritical\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Error thrown: column labels are: {}'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDF\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36msort_values\u001b[0;34m(self, by, axis, ascending, inplace, kind, na_position, ignore_index, key)\u001b[0m\n\u001b[1;32m 5453\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5454\u001b[0m \u001b[0mby\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mby\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 5455\u001b[0;31m \u001b[0mk\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_label_or_level_values\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mby\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 5456\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5457\u001b[0m \u001b[0;31m# need to rewrap column in Series to apply key function\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/pandas/core/generic.py\u001b[0m in \u001b[0;36m_get_label_or_level_values\u001b[0;34m(self, key, axis)\u001b[0m\n\u001b[1;32m 1697\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1698\u001b[0m \u001b[0mlabel_axis_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"column\"\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0maxis\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;34m\"index\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1699\u001b[0;31m raise ValueError(\n\u001b[0m\u001b[1;32m 1700\u001b[0m \u001b[0;34mf\"The {label_axis_name} label '{key}' is not unique.{multi_message}\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1701\u001b[0m )\n", - "\u001b[0;31mValueError\u001b[0m: The column label 'Sample Name' is not unique." - ] - } - ], + "outputs": [], "source": [ "from isatools.isatab import dump\n", "\n", @@ -568,9 +357,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -582,7 +371,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb b/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb index 426fe9d50..f5f6bc801 100644 --- a/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb +++ b/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb @@ -2,132 +2,17 @@ "cells": [ { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "20e0c3cb", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting git+https://github.com/isa-tools/isa-api.git@develop\r\n", - " Cloning https://github.com/isa-tools/isa-api.git (to revision develop) to /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-req-build-5zrvfhbx\r\n", - " Running command git clone --filter=blob:none --quiet https://github.com/isa-tools/isa-api.git /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-req-build-5zrvfhbx\r\n", - " Running command git checkout -b develop --track origin/develop\r\n", - " Switched to a new branch 'develop'\r\n", - " Branch 'develop' set up to track remote branch 'develop' from 'origin'.\r\n", - " Resolved https://github.com/isa-tools/isa-api.git to commit d246d7752e16d16ee41cf5a1024e50e1898924ff\r\n", - " Preparing metadata (setup.py) ... \u001B[?25l-\b \bdone\r\n", - "\u001B[?25hRequirement already satisfied: graphene==3.1.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.1.1)\r\n", - "Requirement already satisfied: graphql-core==3.2.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.2.3)\r\n", - "Requirement already satisfied: wheel~=0.36.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (0.36.2)\r\n", - "Requirement already satisfied: setuptools~=57.1.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (57.1.0)\r\n", - "Requirement already satisfied: numpy~=1.23.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.23.5)\r\n", - "Requirement already satisfied: jsonschema~=4.18.4 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.18.6)\r\n", - "Requirement already satisfied: pandas==1.5.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.5.0)\r\n", - "Requirement already satisfied: openpyxl>=2.5.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.6.4)\r\n", - "Requirement already satisfied: networkx~=2.5.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.5.1)\r\n", - "Requirement already satisfied: lxml~=4.9.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.9.3)\r\n", - "Requirement already satisfied: requests~=2.25.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.25.1)\r\n", - "Requirement already satisfied: iso8601~=0.1.14 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (0.1.16)\r\n", - "Requirement already satisfied: chardet~=4.0.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.0.0)\r\n", - "Requirement already satisfied: jinja2~=3.0.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.0.1)\r\n", - "Requirement already satisfied: beautifulsoup4~=4.9.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.9.3)\r\n", - "Requirement already satisfied: mzml2isa==1.1.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.1.1)\r\n", - "Requirement already satisfied: biopython~=1.79 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.79)\r\n", - "Requirement already satisfied: progressbar2~=3.53.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.53.1)\r\n", - "Requirement already satisfied: deepdiff~=5.5.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (5.5.0)\r\n", - "Requirement already satisfied: PyYAML~=6.0.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (6.0.1)\r\n", - "Requirement already satisfied: bokeh~=2.3.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.3.3)\r\n", - "Requirement already satisfied: certifi==2021.5.30 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2021.5.30)\r\n", - "Requirement already satisfied: flake8==3.9.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.9.2)\r\n", - "Requirement already satisfied: ddt==1.4.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.4.2)\r\n", - "Requirement already satisfied: behave==1.2.6 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.2.6)\r\n", - "Requirement already satisfied: httpretty==1.1.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.1.3)\r\n", - "Requirement already satisfied: sure==2.0.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.0.0)\r\n", - "Requirement already satisfied: coveralls~=3.1.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.1.0)\r\n", - "Requirement already satisfied: rdflib~=6.0.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (6.0.2)\r\n", - "Requirement already satisfied: Flask~=2.2.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.2.5)\r\n", - "Requirement already satisfied: flask_sqlalchemy~=3.0.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.0.5)\r\n", - "Requirement already satisfied: parse-type>=0.4.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from behave==1.2.6->isatools==0.14.2) (0.6.2)\r\n", - "Requirement already satisfied: six>=1.11 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from behave==1.2.6->isatools==0.14.2) (1.16.0)\r\n", - "Requirement already satisfied: parse>=1.8.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from behave==1.2.6->isatools==0.14.2) (1.19.1)\r\n", - "Requirement already satisfied: mccabe<0.7.0,>=0.6.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from flake8==3.9.2->isatools==0.14.2) (0.6.1)\r\n", - "Requirement already satisfied: pycodestyle<2.8.0,>=2.7.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from flake8==3.9.2->isatools==0.14.2) (2.7.0)\r\n", - "Requirement already satisfied: pyflakes<2.4.0,>=2.3.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from flake8==3.9.2->isatools==0.14.2) (2.3.1)\r\n", - "Requirement already satisfied: graphql-relay<3.3,>=3.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from graphene==3.1.1->isatools==0.14.2) (3.2.0)\r\n", - "Requirement already satisfied: aniso8601<10,>=8 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from graphene==3.1.1->isatools==0.14.2) (9.0.1)\r\n", - "Requirement already satisfied: fs~=2.4 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from mzml2isa==1.1.1->isatools==0.14.2) (2.4.13)\r\n", - "Requirement already satisfied: pronto~=2.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from mzml2isa==1.1.1->isatools==0.14.2) (2.5.1)\r\n", - "Requirement already satisfied: pytz>=2020.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from pandas==1.5.0->isatools==0.14.2) (2021.1)\r\n", - "Requirement already satisfied: python-dateutil>=2.8.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from pandas==1.5.0->isatools==0.14.2) (2.8.2)\r\n", - "Requirement already satisfied: mock in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from sure==2.0.0->isatools==0.14.2) (5.1.0)\r\n", - "Requirement already satisfied: soupsieve>1.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from beautifulsoup4~=4.9.3->isatools==0.14.2) (2.2.1)\r\n", - "Requirement already satisfied: pillow>=7.1.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from bokeh~=2.3.2->isatools==0.14.2) (10.1.0)\r\n", - "Requirement already satisfied: tornado>=5.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from bokeh~=2.3.2->isatools==0.14.2) (6.1)\r\n", - "Requirement already satisfied: typing-extensions>=3.7.4 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from bokeh~=2.3.2->isatools==0.14.2) (4.8.0)\r\n", - "Requirement already satisfied: packaging>=16.8 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from bokeh~=2.3.2->isatools==0.14.2) (21.0)\r\n", - "Requirement already satisfied: coverage<6.0,>=4.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from coveralls~=3.1.0->isatools==0.14.2) (5.5)\r\n", - "Requirement already satisfied: docopt>=0.6.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from coveralls~=3.1.0->isatools==0.14.2) (0.6.2)\r\n", - "Requirement already satisfied: ordered-set==4.0.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from deepdiff~=5.5.0->isatools==0.14.2) (4.0.2)\r\n", - "Requirement already satisfied: click>=8.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from Flask~=2.2.2->isatools==0.14.2) (8.1.7)\r\n", - "Requirement already satisfied: itsdangerous>=2.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from Flask~=2.2.2->isatools==0.14.2) (2.1.2)\r\n", - "Requirement 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in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from progressbar2~=3.53.1->isatools==0.14.2) (2.5.6)\r\n", - "Requirement already satisfied: pyparsing in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from rdflib~=6.0.2->isatools==0.14.2) (2.4.7)\r\n", - "Requirement already satisfied: isodate in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from rdflib~=6.0.2->isatools==0.14.2) (0.6.0)\r\n", - "Requirement already satisfied: idna<3,>=2.5 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from requests~=2.25.1->isatools==0.14.2) (2.10)\r\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from requests~=2.25.1->isatools==0.14.2) (1.26.6)\r\n", - "Requirement already satisfied: appdirs~=1.4.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from fs~=2.4->mzml2isa==1.1.1->isatools==0.14.2) (1.4.4)\r\n", - "Requirement already satisfied: zipp>=0.5 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from importlib-metadata>=3.6.0->Flask~=2.2.2->isatools==0.14.2) (3.17.0)\r\n", - "Requirement already satisfied: fastobo~=0.12.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from pronto~=2.0->mzml2isa==1.1.1->isatools==0.14.2) (0.12.2)\r\n", - "Requirement already satisfied: greenlet!=0.4.17 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from sqlalchemy>=1.4.18->flask_sqlalchemy~=3.0.2->isatools==0.14.2) (3.0.1)\r\n", - "Building wheels for collected packages: isatools\r\n", - " Building wheel for isatools (setup.py) ... \u001B[?25l-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \b/\b \b-\b \b\\\b \b|\b \bdone\r\n", - "\u001B[?25h Created wheel for isatools: filename=isatools-0.14.2-py3-none-any.whl size=2687364 sha256=a1e03f45642a270ed616ebe1fabe6fd2c9b92e720b4335ff97dfd2f14dbaa21c\r\n", - " Stored in directory: /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-ephem-wheel-cache-blllffov/wheels/7a/cd/2f/2a642c74c35b34fbde447e2b8bbf6ec194796d0c6ef5571318\r\n", - "Successfully built isatools\r\n", - "Installing collected packages: isatools\r\n", - " Attempting uninstall: isatools\r\n", - " Found existing installation: isatools 0.12.0a0\r\n", - "\u001B[31mERROR: Exception:\r\n", - "Traceback (most recent call last):\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/cli/base_command.py\", line 167, in exc_logging_wrapper\r\n", - " status = run_func(*args)\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/cli/req_command.py\", line 205, in wrapper\r\n", - " return func(self, options, args)\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/commands/install.py\", line 405, in run\r\n", - " installed = install_given_reqs(\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/__init__.py\", line 68, in install_given_reqs\r\n", - " uninstalled_pathset = requirement.uninstall(auto_confirm=True)\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/req_install.py\", line 637, in uninstall\r\n", - " uninstalled_pathset = UninstallPathSet.from_dist(dist)\r\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/req_uninstall.py\", line 530, in from_dist\r\n", - " assert link_pointer == dist_location, (\r\n", - "AssertionError: Egg-link /Users/philippe/Documents/git/isa-api2/isa-api/src/isatools does not match installed location of isatools (at /Users/philippe/Documents/git/isa-api2/isa-api)\u001B[0m\u001B[31m\r\n", - "\u001B[0m\u001B[33mWARNING: You are using pip version 22.0.3; however, version 23.3.1 is available.\r\n", - "You should consider upgrading via the '/Users/philippe/.pyenv/versions/3.9.0/bin/python3.9 -m pip install --upgrade pip' command.\u001B[0m\u001B[33m\r\n", - "\u001B[0m" - ] - } - ], + "outputs": [], "source": [ "!pip install git+https://github.com/isa-tools/isa-api.git@develop" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "7f776e9d", "metadata": {}, "outputs": [], @@ -161,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "cc70ba63", "metadata": {}, "outputs": [], @@ -178,70 +63,39 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "id": "7931bbd0", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Name: isatools\r\n", - "Version: 0.12.0a0\r\n", - "Summary: Metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments\r\n", - "Home-page: https://github.com/ISA-tools/isa-api\r\n", - "Author: ISA Infrastructure Team\r\n", - "Author-email: isatools@googlegroups.com\r\n", - "License: UNKNOWN\r\n", - "Location: /Users/philippe/Documents/git/isa-api2/isa-api\r\n", - "Requires: beautifulsoup4, biopython, chardet, deepdiff, iso8601, jinja2, jsonschema, lxml, mzml2isa, networkx, numpy, pandas, progressbar2, PyYAML, requests\r\n", - "Required-by: \r\n" - ] - } - ], + "outputs": [], "source": [ "!pip show isatools" ] }, { "cell_type": "code", - "execution_count": 16, - "outputs": [], - "source": [ - "main_path = \"./output/ISA-BH2023-ALL/\"\n", - "data_path = \"./notebook-output/BII-I-1-RT/\"" - ], + "execution_count": null, + "id": "a3676e04", "metadata": { "collapsed": false, + "jupyter": { + "outputs_hidden": false + }, "pycharm": { "name": "#%%\n" } - } + }, + "outputs": [], + "source": [ + "main_path = \"./output/ISA-BH2023-ALL/\"\n", + "data_path = \"./notebook-output/BII-I-1-RT/\"" + ] }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "id": "a2a84bfd", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CONFIG at: /Users/philippe/Documents/git/isa-api2/isa-api/isatools/isajson/../resources/config/json/default\n", - "assay name: spectrum.mzdata\n", - "assay name: proteins.csv\n", - "assay name: ptms.csv\n", - "assay name: peptides.csv\n", - "assay name: PRIDE_Exp_Complete_Ac_8761.xml\n", - "assay name: JIC85_Sulphate_0.10_External_1_1.txt\n", - "assay name: E-MEXP-115-raw-data-331224145.txt\n", - "assay name: E-MEXP-115-processed-data-1341986893.txt\n", - "assay name: E-MAXD-4-raw-data-426648675.txt\n", - "assay name: E-MAXD-4-processed-data-1342566476.txt\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import json2isatab\n", "with open(os.path.join(\"./../../../tests/data/json/BII-I-1\", \"BII-I-1.json\")) as json_fp:\n", @@ -252,7 +106,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "id": "ec7f914a", "metadata": {}, "outputs": [], @@ -263,13 +117,21 @@ "with open(os.path.join(data_path, 'isa.json'), 'w') as out_fp:\n", " json.dump(isa_json, out_fp)" ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "382f8f10-efed-43f2-9fa6-6d6d12417f0d", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { "kernelspec": { - "name": "isa-py-3.11", + "display_name": "Python 3 (ipykernel)", "language": "python", - "display_name": "isa-py-3.11" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -281,9 +143,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/isa-cookbook/content/notebooks/create-a-repeated-treatment-design-with-ISA-descriptor.ipynb b/isa-cookbook/content/notebooks/create-a-repeated-treatment-design-with-ISA-descriptor.ipynb index 6326028b5..631fbd63b 100644 --- a/isa-cookbook/content/notebooks/create-a-repeated-treatment-design-with-ISA-descriptor.ipynb +++ b/isa-cookbook/content/notebooks/create-a-repeated-treatment-design-with-ISA-descriptor.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -34,7 +34,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": { "scrolled": true }, @@ -76,7 +76,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": { "scrolled": true }, @@ -101,7 +101,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": { "scrolled": true }, @@ -113,7 +113,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": { "scrolled": true }, @@ -133,7 +133,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": { "scrolled": true }, @@ -169,22 +169,11 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "NonTreatment(\n", - " type='screen',\n", - " duration=isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=0.0, unit=isatools.model.OntologyAnnotation(term='days', term_source=None, term_accession='', comments=[]))\n", - " )\n" - ] - } - ], + "outputs": [], "source": [ "nte1 = NonTreatment(element_type='screen', duration_unit=OntologyAnnotation(term=\"days\"))\n", "print(nte1)" @@ -199,22 +188,11 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=biological intervention, \n", - " factor_values=[])\n", - " \n" - ] - } - ], + "outputs": [], "source": [ "te1 = Treatment()\n", "te1.type='biological intervention'\n", @@ -232,7 +210,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": { "scrolled": true }, @@ -248,22 +226,11 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=biological intervention, \n", - " factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='quantity', term_source=None, term_accession='', comments=[]), comments=[]), value='high dose', unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='time post infection', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=isatools.model.OntologyAnnotation(term='hr', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='virus', factor_type=isatools.model.OntologyAnnotation(term='organism', term_source=None, term_accession='', comments=[]), comments=[]), value='hsv1', unit=None)])\n", - " \n" - ] - } - ], + "outputs": [], "source": [ "#assigning the factor values declared above to the ISA treatment element\n", "te1.factor_values = [f1v,f2v,f3v]\n", @@ -279,22 +246,11 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=chemical intervention, \n", - " factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='antiviral', factor_type=isatools.model.OntologyAnnotation(term='chemical entity', term_source=None, term_accession='', comments=[]), comments=[]), value='hsvflumab', unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='quantity', term_source=None, term_accession='', comments=[]), comments=[]), value=10, unit=isatools.model.OntologyAnnotation(term='mg/kg/day', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='treatment duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=isatools.model.OntologyAnnotation(term='weeks', term_source=None, term_accession='', comments=[]))])\n", - " \n" - ] - } - ], + "outputs": [], "source": [ "te2 = Treatment()\n", "te2.type = 'chemical intervention'\n", @@ -312,22 +268,11 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=radiological intervention, \n", - " factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='quantity', term_source=None, term_accession='', comments=[]), comments=[]), value='10', unit=isatools.model.OntologyAnnotation(term='mSev', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='radiation', factor_type=isatools.model.OntologyAnnotation(term='physical entity', term_source=None, term_accession='', comments=[]), comments=[]), value='neutron beam', unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='treatment duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value='30', unit=isatools.model.OntologyAnnotation(term='minutes', term_source=None, term_accession='', comments=[]))])\n", - " \n" - ] - } - ], + "outputs": [], "source": [ "te3 = Treatment()\n", "te3.type = 'radiological intervention'\n", @@ -351,19 +296,11 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "screen\n" - ] - } - ], + "outputs": [], "source": [ "# Creation of another ISA element, which is not a Treatment element, which is of type `screen` by default\n", "nte2 = NonTreatment(duration_unit=OntologyAnnotation(term=\"days\"))\n", @@ -372,19 +309,11 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "run-in\n" - ] - } - ], + "outputs": [], "source": [ "# let's change it by setting its type by relying on the keys defined for the object\n", "nte2.type=RUN_IN\n", @@ -393,19 +322,11 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "washout\n" - ] - } - ], + "outputs": [], "source": [ "#let's change it again by direct use of the allowed strings (note: the string should match exactly the predefined values)\n", "nte2.type = WASHOUT\n", @@ -414,7 +335,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": { "scrolled": true }, @@ -434,22 +355,11 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "NonTreatment(\n", - " type='follow-up',\n", - " duration=isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=4, unit=isatools.model.OntologyAnnotation(term='month', term_source=None, term_accession='', comments=[]))\n", - " )\n" - ] - } - ], + "outputs": [], "source": [ "nte3 = NonTreatment(element_type=FOLLOW_UP, duration_value=4, duration_unit=OntologyAnnotation(term=\"month\"))\n", "# nte3.duration.value = 2\n", @@ -467,7 +377,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": { "scrolled": true }, @@ -491,42 +401,11 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"StudyArm(\n", - " name=Arm 1,\n", - " source_type=Characteristic(\n", - " category=Study Subject\n", - " value=Human\n", - " unit=\n", - " comments=0 Comment objects\n", - "),\n", - " group_size=5, \n", - " no. cells=0,\n", - " no. sample_assay_plans=0\n", - " )\n", - "\"StudyArm(\n", - " name=Arm 1,\n", - " source_type=Characteristic(\n", - " category=genotype\n", - " value=control - normal\n", - " unit=\n", - " comments=0 Comment objects\n", - "),\n", - " group_size=2, \n", - " no. cells=0,\n", - " no. sample_assay_plans=0\n", - " )\n" - ] - } - ], + "outputs": [], "source": [ "arm1 = StudyArm(name='Arm 1', group_size=5, )\n", "print(arm1)\n", @@ -555,7 +434,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": { "scrolled": true }, @@ -581,7 +460,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": { "scrolled": true }, @@ -634,7 +513,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -654,7 +533,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": { "scrolled": true }, @@ -706,7 +585,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": { "scrolled": true }, @@ -731,7 +610,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "metadata": { "scrolled": true }, @@ -743,7 +622,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": null, "metadata": { "scrolled": true }, @@ -755,7 +634,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "metadata": { "scrolled": true }, @@ -779,24 +658,11 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Arm 1 Characteristic(\n", - " category=genotype\n", - " value=control - normal\n", - " unit=\n", - " comments=0 Comment objects\n", - ")\n" - ] - } - ], + "outputs": [], "source": [ "arm1.add_item_to_arm_map(st_cl1,sap1)\n", "print(arm1.name, arm1.source_type)" @@ -812,7 +678,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "metadata": { "scrolled": true }, @@ -823,7 +689,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": null, "metadata": { "scrolled": true }, @@ -846,7 +712,7 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": null, "metadata": { "scrolled": true }, @@ -871,7 +737,7 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": null, "metadata": { "scrolled": true }, @@ -903,7 +769,7 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": null, "metadata": { "scrolled": true }, @@ -915,7 +781,7 @@ }, { "cell_type": "code", - "execution_count": 34, + "execution_count": null, "metadata": { "scrolled": true }, @@ -930,7 +796,7 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": null, "metadata": { "scrolled": true }, @@ -955,7 +821,7 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": null, "metadata": { "scrolled": true }, @@ -986,7 +852,7 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1121,7 +987,7 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1131,27 +997,16 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "2" - ] - }, - "execution_count": 39, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "len(study.assays)" ] }, { "cell_type": "code", - "execution_count": 40, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1160,29 +1015,9 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Assay(\n", - " measurement_type=protein profiling\n", - " technology_type=Western blot\n", - " technology_platform=\n", - " filename=a_WB_protein-profiling_Western-blot.txt\n", - " data_files=252 DataFile objects\n", - " samples=0 Sample objects\n", - " process_sequence=504 Process objects\n", - " other_material=252 Material objects\n", - " characteristic_categories=0 OntologyAnnots\n", - " comments=0 Comment objects\n", - " units=0 Unit objects\n", - ")\n" - ] - } - ], + "outputs": [], "source": [ "# print(investigation.studies[0].assays[1])\n", "print(investigation.studies[0].assays[0])" @@ -1190,7 +1025,7 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1200,34 +1035,9 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 18:16:26,476 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0, 1, 2]\n", - "2021-07-21 18:16:26,735 [WARNING]: isatab.py(write_study_table_files:1195) >> [4, 3, 0, 6, 5, 8, 7, 10, 9, 12, 11, 14, 13, 16, 15, 18, 17, 20, 19, 22, 21, 24, 23, 26, 25, 28, 27, 30, 29, 32, 31, 34, 33, 36, 35, 38, 37, 40, 39, 42, 41, 44, 43, 46, 45, 48, 47, 50, 49, 52, 51, 54, 53, 56, 55, 58, 57, 60, 59, 62, 61, 64, 63, 66, 65, 68, 67, 70, 69, 72, 71, 74, 73, 76, 75, 78, 77, 80, 79, 82, 81, 84, 83, 86, 85, 88, 87, 90, 89, 92, 91, 94, 93, 96, 95, 98, 97, 100, 99, 102, 101, 104, 103, 106, 105, 108, 107, 110, 109, 112, 111, 114, 113, 116, 115, 118, 117, 120, 119, 122, 121, 124, 123, 126, 125, 128, 127, 130, 129, 132, 131, 134, 133, 136, 135, 138, 137, 140, 139, 142, 141, 144, 143, 1, 146, 145, 148, 147, 150, 149, 152, 151, 154, 153, 156, 155, 158, 157, 160, 159, 162, 161, 164, 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"\u001b[0;32m/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/ipykernel_18651/1244306393.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0misatools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misatab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdump_tables_to_dataframes\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mdumpdf\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mdataframes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdumpdf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3\u001b[0m \u001b[0mdataframes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mdump_tables_to_dataframes\u001b[0;34m(isa_obj)\u001b[0m\n\u001b[1;32m 4578\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4579\u001b[0m \u001b[0mtmp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtempfile\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmkdtemp\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4580\u001b[0;31m \u001b[0mdump\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0misa_obj\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0misa_obj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtmp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mskip_dump_tables\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4581\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0ms_file\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mglob\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miglob\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtmp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m's_*'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4582\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbasename\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mread_tfile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mdump\u001b[0;34m(isa_obj, output_path, i_file_name, skip_dump_tables, write_factor_values_in_assay_table)\u001b[0m\n\u001b[1;32m 1047\u001b[0m \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1048\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1049\u001b[0;31m \u001b[0mwrite_study_table_files\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1050\u001b[0m write_assay_table_files(\n\u001b[1;32m 1051\u001b[0m investigation, output_path, write_factor_values_in_assay_table)\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_study_table_files\u001b[0;34m(inv_obj, output_dir)\u001b[0m\n\u001b[1;32m 1296\u001b[0m fvlabel = \"{0}.Factor Value[{1}]\".format(\n\u001b[1;32m 1297\u001b[0m olabel, fv.factor_name.name)\n\u001b[0;32m-> 1298\u001b[0;31m \u001b[0mwrite_value_columns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfvlabel\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1299\u001b[0m \"\"\"if isinstance(pbar, ProgressBar):\n\u001b[1;32m 1300\u001b[0m pbar.finish()\"\"\"\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_value_columns\u001b[0;34m(df_dict, label, x)\u001b[0m\n\u001b[1;32m 1717\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1718\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mOntologyAnnotation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1719\u001b[0;31m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1720\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mterm\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1721\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit.Term Source REF\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mKeyError\u001b[0m: 'Sample Name.0.Factor Value[DURATION]'" - ] - } - ], + "outputs": [], "source": [ "# from isatools.isatab import dump_tables_to_dataframes as dumpdf\n", "# dataframes = dumpdf(investigation)\n", @@ -1236,37 +1046,13 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-08-09 18:51:57,184 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0, 1, 2]\n", - "2021-08-09 18:51:57,468 [WARNING]: isatab.py(write_study_table_files:1194) >> [4, 3, 0, 6, 5, 8, 7, 10, 9, 12, 11, 14, 13, 16, 15, 18, 17, 20, 19, 22, 21, 24, 23, 26, 25, 28, 27, 30, 29, 32, 31, 34, 33, 36, 35, 38, 37, 40, 39, 42, 41, 44, 43, 46, 45, 48, 47, 50, 49, 52, 51, 54, 53, 56, 55, 58, 57, 60, 59, 62, 61, 64, 63, 66, 65, 68, 67, 70, 69, 72, 71, 74, 73, 76, 75, 78, 77, 80, 79, 82, 81, 84, 83, 86, 85, 88, 87, 90, 89, 92, 91, 94, 93, 96, 95, 98, 97, 100, 99, 102, 101, 104, 103, 106, 105, 108, 107, 110, 109, 112, 111, 114, 113, 116, 115, 118, 117, 120, 119, 122, 121, 124, 123, 126, 125, 128, 127, 130, 129, 132, 131, 134, 133, 136, 135, 138, 137, 140, 139, 142, 141, 144, 143, 1, 146, 145, 148, 147, 150, 149, 152, 151, 154, 153, 156, 155, 158, 157, 160, 159, 162, 161, 164, 163, 166, 165, 168, 167, 170, 169, 172, 171, 174, 173, 176, 175, 178, 177, 180, 179, 182, 181, 184, 183, 186, 185, 188, 187, 190, 189, 192, 191, 194, 193, 196, 195, 198, 197, 200, 199, 202, 201, 204, 203, 206, 205, 208, 207, 210, 209, 212, 211, 214, 213, 216, 215, 218, 217, 220, 219, 222, 221, 224, 223, 226, 225, 228, 227, 230, 229, 232, 231, 234, 233, 236, 235, 238, 237, 240, 239, 242, 241, 244, 243, 246, 245, 248, 247, 250, 249, 252, 251, 254, 253, 256, 255, 258, 257, 260, 259, 262, 261, 264, 263, 266, 265, 268, 267, 270, 269, 272, 271, 274, 273, 276, 275, 278, 277, 280, 279, 282, 281, 284, 283, 286, 285, 288, 287, 290, 289, 292, 291, 294, 293, 296, 295, 298, 297, 300, 299, 302, 301, 304, 303, 306, 305, 308, 307, 310, 309, 312, 311, 314, 313, 316, 315, 318, 317, 320, 319, 322, 321, 324, 323, 326, 325, 328, 327, 330, 329, 332, 331, 334, 333, 336, 335, 338, 337, 340, 339, 342, 341, 344, 343, 346, 345, 348, 347, 350, 349, 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749, 752, 751, 754, 753, 756, 755, 758, 757, 760, 759, 762, 761, 764, 763, 766, 765, 768, 767, 770, 769, 772, 771, 774, 773, 776, 775, 778, 777, 780, 779, 782, 781, 784, 783, 786, 785, 788, 787, 790, 789, 792, 791, 794, 793, 796, 795, 798, 797, 800, 799, 802, 801, 804, 803, 806, 805, 808, 807, 810, 809, 812, 811, 814, 813, 816, 815, 818, 817, 820, 819, 822, 821, 824, 823, 826, 825, 828, 827, 830, 829, 832, 831, 834, 833, 836, 835, 838, 837, 840, 839, 842, 841]\n", - "2021-08-09 18:51:57,471 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[0, 4, 3], [0, 6, 5], [0, 8, 7], [0, 10, 9], [0, 12, 11], [0, 14, 13], [0, 16, 15], [0, 18, 17], [0, 20, 19], [0, 22, 21], [0, 24, 23], [0, 26, 25], [0, 28, 27], [0, 30, 29], [0, 32, 31], [0, 34, 33], [0, 36, 35], [0, 38, 37], [0, 40, 39], [0, 42, 41], [0, 44, 43], [0, 46, 45], [0, 48, 47], [0, 50, 49], [0, 52, 51], [0, 54, 53], [0, 56, 55], [0, 58, 57], [0, 60, 59], [0, 62, 61], [0, 64, 63], [0, 66, 65], [0, 68, 67], [0, 70, 69], [0, 72, 71], [0, 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"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/ipykernel_54507/4200718032.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;31m# import os\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;31m# os.makedirs('/notebook-output/isa-repeated-measure-crossover-design', exist_ok = True)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0misatab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdump\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'./notebook-output/isa-repeated-measure-crossover-design'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mdump\u001b[0;34m(isa_obj, output_path, i_file_name, skip_dump_tables, write_factor_values_in_assay_table)\u001b[0m\n\u001b[1;32m 1047\u001b[0m \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1048\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1049\u001b[0;31m \u001b[0mwrite_study_table_files\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1050\u001b[0m write_assay_table_files(\n\u001b[1;32m 1051\u001b[0m investigation, output_path, write_factor_values_in_assay_table)\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_study_table_files\u001b[0;34m(inv_obj, output_dir)\u001b[0m\n\u001b[1;32m 1295\u001b[0m fvlabel = \"{0}.Factor Value[{1}]\".format(\n\u001b[1;32m 1296\u001b[0m olabel, fv.factor_name.name)\n\u001b[0;32m-> 1297\u001b[0;31m \u001b[0mwrite_value_columns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfvlabel\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1298\u001b[0m \"\"\"if isinstance(pbar, ProgressBar):\n\u001b[1;32m 1299\u001b[0m pbar.finish()\"\"\"\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/src/isatools/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_value_columns\u001b[0;34m(df_dict, label, x)\u001b[0m\n\u001b[1;32m 1715\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1716\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mOntologyAnnotation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1717\u001b[0;31m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1718\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mterm\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1719\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit.Term Source REF\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mKeyError\u001b[0m: 'Sample Name.0.Factor Value[DURATION]'" - ] - } - ], + "outputs": [], "source": [ "# Alternatevely, if you want to save the ISA-TAB files to a specific directory, you can run:\n", "from isatools import isatab\n", @@ -1344,9 +1130,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -1358,9 +1144,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, - "nbformat_minor": 1 + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor-test-json.ipynb b/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor-test-json.ipynb index 1bbf9890d..8f0e3c87a 100644 --- a/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor-test-json.ipynb +++ b/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor-test-json.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -25,7 +25,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62,7 +62,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -140,7 +140,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -229,52 +229,9 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[], publications=[], contacts=[], studies=[isatools.model.Study(filename='s_study.txt', identifier='S1', title='My Simple ISA Study', description='We could alternatively use the class constructor's parameters to set some default values at the time of creation, however we want to demonstrate how to use the object's instance variables to set values.', submission_date='2021-12-01 22:29:22.101893', public_release_date='2021-12-01 22:29:22.101933', contacts=[isatools.model.Person(last_name='hughes', first_name='bob', mid_initials='', email='bob.hughes@who.else', phone='', fax='', address='', affiliation='WHO', roles=[], comments=[isatools.model.Comment(name='per_comment', value='per_value')])], design_descriptors=[], publications=[isatools.model.Publication(pubmed_id='1222322', doi='10.12314', author_list='', title='publication title', status=None, comments=[])], factors=[isatools.model.StudyFactor(name='Factor', factor_type=isatools.model.OntologyAnnotation(term='factor category', term_source=None, term_accession='', comments=[]), comments=[])], protocols=[isatools.model.Protocol(name='sample collection', protocol_type=isatools.model.OntologyAnnotation(term='', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='data analysis with Galaxy', protocol_type=isatools.model.OntologyAnnotation(term='data transformation', term_source=None, term_accession='', comments=[]), uri='https://doi.org/10.5464/workflow.cwl', version='', parameters=[isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='genome assembly', term_source=None, term_accession='', comments=[]), comments=[]), isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='cut-off value', term_source=None, term_accession='', comments=[]), comments=[])], components=[], comments=[]), isatools.model.Protocol(name='data visualization with Intermine', protocol_type=isatools.model.OntologyAnnotation(term='data visualization', term_source=None, term_accession='', comments=[]), uri='https://intermine.org/10.5464/network.svg', version='', parameters=[], components=[], comments=[isatools.model.Comment(name='pro_comment', value='pro_value')]), isatools.model.Protocol(name='extraction', protocol_type=isatools.model.OntologyAnnotation(term='material extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='extraction', protocol_type=isatools.model.OntologyAnnotation(term='material extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='sequencing', protocol_type=isatools.model.OntologyAnnotation(term='material sequencing', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[])], assays=[isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='genome sequencing', term_source=None, term_accession='', comments=[]), technology_type=isatools.model.OntologyAnnotation(term='nucleotide sequencing', term_source=None, term_accession='', comments=[]), technology_platform='', filename='a_assay.txt', data_files=[isatools.model.DataFile(filename='sequenced-data-0', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='data_comment', value='data_value')])], samples=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[isatools.model.Source(name='source1', characteristics=[], comments=[isatools.model.Comment(name='src_comment', value='src_value')]), isatools.model.Source(name='source2', characteristics=[], comments=[])], comments=[isatools.model.Comment(name='smp_comment', value='smp_value')])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=extraction\n", - " protocol_type=material extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[isatools.model.Source(name='source1', characteristics=[], comments=[isatools.model.Comment(name='src_comment', value='src_value')]), isatools.model.Source(name='source2', characteristics=[], comments=[])], comments=[isatools.model.Comment(name='smp_comment', value='smp_value')])], outputs=[]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=labeling\n", - " protocol_type=labeling\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-0\", executes_protocol=Protocol(\n", - " name=sequencing\n", - " protocol_type=material sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-0', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='data_comment', value='data_value')])])], other_material=[, ], characteristic_categories=[], comments=[], units=[])], sources=[isatools.model.Source(name='source1', characteristics=[], comments=[isatools.model.Comment(name='src_comment', value='src_value')]), isatools.model.Source(name='source2', characteristics=[], comments=[])], samples=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[isatools.model.Source(name='source1', characteristics=[], comments=[isatools.model.Comment(name='src_comment', value='src_value')]), isatools.model.Source(name='source2', characteristics=[], comments=[])], comments=[isatools.model.Comment(name='smp_comment', value='smp_value')])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=data visualization with Intermine\n", - " protocol_type=data visualization\n", - " uri=https://intermine.org/10.5464/network.svg\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=1 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='source2', characteristics=[], comments=[])], outputs=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[isatools.model.Source(name='source1', characteristics=[], comments=[isatools.model.Comment(name='src_comment', value='src_value')]), isatools.model.Source(name='source2', characteristics=[], comments=[])], comments=[isatools.model.Comment(name='smp_comment', value='smp_value')])])], other_material=[], characteristic_categories=[], comments=[isatools.model.Comment(name='st_comment', value='st_value')], units=[])], comments=[isatools.model.Comment(name='i_comment', value='i_value')])" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Let's see the object :\n", "investigation" @@ -289,133 +246,9 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-12-01 22:29:22,205 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [1]\n", - "2021-12-01 22:29:22,206 [WARNING]: isatab.py(write_study_table_files:1194) >> [3, 2, 1]\n", - "2021-12-01 22:29:22,207 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[1, 3, 2]]\n", - "2021-12-01 22:29:22,229 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2]\n", - "2021-12-01 22:29:22,230 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 4, 5, 6, 7, 8]]\n", - "2021-12-01 22:29:22,230 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 4, 5, 6, 7, 8]]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmpkd97rbgg/i_investigation.txt\n", - "ONTOLOGY SOURCE REFERENCE\n", - "Term Source Name\n", - "Term Source File\n", - "Term Source Version\n", - "Term Source Description\n", - "INVESTIGATION\n", - "Investigation Identifier\t\n", - "Investigation Title\t\n", - "Investigation Description\t\n", - "Investigation Submission Date\t\n", - "Investigation Public Release Date\t\n", - "Comment[i_comment]\ti_value\n", - "INVESTIGATION PUBLICATIONS\n", - "Investigation PubMed ID\n", - "Investigation Publication DOI\n", - "Investigation Publication Author List\n", - "Investigation Publication Title\n", - "Investigation Publication Status\n", - "Investigation Publication Status Term Accession Number\n", - "Investigation Publication Status Term Source REF\n", - "INVESTIGATION CONTACTS\n", - "Investigation Person Last Name\n", - "Investigation Person First Name\n", - "Investigation Person Mid Initials\n", - "Investigation Person Email\n", - "Investigation Person Phone\n", - "Investigation Person Fax\n", - "Investigation Person Address\n", - "Investigation Person Affiliation\n", - "Investigation Person Roles\n", - "Investigation Person Roles Term Accession Number\n", - "Investigation Person Roles Term Source REF\n", - "STUDY\n", - "Study Identifier\tS1\n", - "Study Title\tMy Simple ISA Study\n", - "Study Description\tWe could alternatively use the class constructor's parameters to set some default values at the time of creation, however we want to demonstrate how to use the object's instance variables to set values.\n", - "Study Submission Date\t2021-12-01 22:29:22.101893\n", - "Study Public Release Date\t2021-12-01 22:29:22.101933\n", - "Study File Name\ts_study.txt\n", - "Comment[st_comment]\tst_value\n", - "STUDY DESIGN DESCRIPTORS\n", - "Study Design Type\n", - "Study Design Type Term Accession Number\n", - "Study Design Type Term Source REF\n", - "STUDY PUBLICATIONS\n", - "Study PubMed ID\t1222322\n", - "Study Publication DOI\t10.12314\n", - "Study Publication Author List\t\n", - "Study Publication Title\tpublication title\n", - "Study Publication Status\t\n", - "Study Publication Status Term Accession Number\t\n", - "Study Publication Status Term Source REF\t\n", - "STUDY FACTORS\n", - "Study Factor Name\tFactor\n", - "Study Factor Type\tfactor category\n", - "Study Factor Type Term Accession Number\t\n", - "Study Factor Type Term Source REF\t\n", - "STUDY ASSAYS\n", - "Study Assay File Name\ta_assay.txt\n", - "Study Assay Measurement Type\tgenome sequencing\n", - "Study Assay Measurement Type Term Accession Number\t\n", - "Study Assay Measurement Type Term Source REF\t\n", - "Study Assay Technology Type\tnucleotide sequencing\n", - "Study Assay Technology Type Term Accession Number\t\n", - "Study Assay Technology Type Term Source REF\t\n", - "Study Assay Technology Platform\t\n", - "STUDY PROTOCOLS\n", - "Study Protocol Name\tsample collection\tdata analysis with Galaxy\tdata visualization with Intermine\textraction\textraction\tsequencing\n", - "Study Protocol Type\t\tdata transformation\tdata visualization\tmaterial extraction\tmaterial extraction\tmaterial sequencing\n", - "Study Protocol Type Term Accession Number\t\t\t\t\t\t\n", - "Study Protocol Type Term Source REF\t\t\t\t\t\t\n", - "Study Protocol Description\t\t\t\t\t\t\n", - "Study Protocol URI\t\thttps://doi.org/10.5464/workflow.cwl\thttps://intermine.org/10.5464/network.svg\t\t\t\n", - "Study Protocol Version\t\t\t\t\t\t\n", - "Study Protocol Parameters Name\t\tgenome assembly;cut-off value\t\t\t\t\n", - "Study Protocol Parameters Name Term Accession Number\t\t;\t\t\t\t\n", - "Study Protocol Parameters Name Term Source REF\t\t;\t\t\t\t\n", - "Study Protocol Components Name\t\t\t\t\t\t\n", - "Study Protocol Components Type\t\t\t\t\t\t\n", - "Study Protocol Components Type Term Accession Number\t\t\t\t\t\t\n", - "Study Protocol Components Type Term Source REF\t\t\t\t\t\t\n", - "Comment[pro_comment]\t\t\tpro_value\t\t\t\n", - "STUDY CONTACTS\n", - "Study Person Last Name\thughes\n", - "Study Person First Name\tbob\n", - "Study Person Mid Initials\t\n", - "Study Person Email\tbob.hughes@who.else\n", - "Study Person Phone\t\n", - "Study Person Fax\t\n", - "Study Person Address\t\n", - "Study Person Affiliation\tWHO\n", - "Study Person Roles\t\n", - "Study Person Roles Term Accession Number\t\n", - "Study Person Roles Term Source REF\t\n", - "Comment[per_comment]\tper_value\n", - "--------\n", - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmpkd97rbgg/s_study.txt\n", - "Source Name\tProtocol REF\tSample Name\tComment[smp_comment]\n", - "source2\tdata visualization with Intermine\tsample1\tsmp_value\n", - "--------\n", - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmpkd97rbgg/a_assay.txt\n", - "Sample Name\tComment[smp_comment]\tProtocol REF\tExtract Name\tComment[mat_comment]\tProtocol REF\tLabeled Extract Name\tProtocol REF\tRaw Data File\tComment[data_comment]\n", - "sample1\tsmp_value\textraction\textract-0\tmat_value\tlabeling\tlabeleddextract-0\tsequencing\tsequenced-data-0\tdata_value\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.isatab import dumps\n", "print(dumps(investigation))" @@ -430,440 +263,9 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"@id\": \"#investigation/4909215360\",\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"i_comment\",\n", - " \"value\": \"i_value\"\n", - " }\n", - " ],\n", - " \"description\": \"\",\n", - " \"identifier\": \"\",\n", - " \"ontologySourceReferences\": [],\n", - " \"people\": [],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studies\": [\n", - " {\n", - " \"@id\": \"#study/4909211904\",\n", - " \"assays\": [\n", - " {\n", - " \"@id\": \"#4909152096\",\n", - " \"characteristicCategories\": [],\n", - " \"comments\": [],\n", - " \"dataFiles\": [\n", - " {\n", - " \"@id\": \"#data/rawdata-4357026720\",\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"data_comment\",\n", - " \"value\": \"data_value\"\n", - " }\n", - " ],\n", - " \"name\": \"sequenced-data-0\",\n", - " \"type\": \"Raw Data File\"\n", - " }\n", - " ],\n", - " \"filename\": \"a_assay.txt\",\n", - " \"materials\": {\n", - " \"otherMaterials\": [\n", - " {\n", - " \"@id\": \"#material/extract-4357027824\",\n", - " \"characteristics\": [],\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"mat_comment\",\n", - " \"value\": \"mat_value\"\n", - " }\n", - " ],\n", - " \"name\": \"extract-0\",\n", - " \"type\": \"Extract Name\"\n", - " },\n", - " {\n", - " \"@id\": \"#material/labeledextract-4357027488\",\n", - " \"characteristics\": [],\n", - " \"comments\": [],\n", - " \"name\": \"labeleddextract-0\",\n", - " \"type\": \"Labeled Extract Name\"\n", - " }\n", - " ],\n", - " \"samples\": [\n", - " {\n", - " \"@id\": \"#sample/4909191280\",\n", - " \"characteristics\": [],\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"smp_comment\",\n", - " \"value\": \"smp_value\"\n", - " }\n", - " ],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample1\"\n", - " }\n", - " ]\n", - " },\n", - " \"measurementType\": {\n", - " \"@id\": \"#annotation_value/33b03c28-95c0-4f2c-8755-9986e71e9290\",\n", - " \"annotationValue\": \"genome sequencing\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"processSequence\": [\n", - " {\n", - " \"@id\": \"#process/4357029072\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#protocol/4909154064\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#sample/4909191280\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/4357027536\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-4357027824\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#process/4357027536\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#protocol/4909153968\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-4357027824\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/4357026672\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#material/labeledextract-4357027488\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\",\n", - " \"previousProcess\": {\n", - " \"@id\": \"#process/4357029072\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#process/4357026672\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#protocol/4909153920\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#material/labeledextract-4357027488\"\n", - " }\n", - " ],\n", - " \"name\": \"assay-name-0\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#data/rawdata-4357026720\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\",\n", - " \"previousProcess\": {\n", - " \"@id\": \"#process/4357027536\"\n", - " }\n", - " }\n", - " ],\n", - " \"technologyPlatform\": \"\",\n", - " \"technologyType\": {\n", - " \"@id\": \"#annotation_value/5174e4a8-f267-480d-930f-998f81064712\",\n", - " \"annotationValue\": \"nucleotide sequencing\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"characteristicCategories\": [],\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"st_comment\",\n", - " \"value\": \"st_value\"\n", - " }\n", - " ],\n", - " \"description\": \"We could alternatively use the class constructor's parameters to set some default values at the time of creation, however we want to demonstrate how to use the object's instance variables to set values.\",\n", - " \"factors\": [\n", - " {\n", - " \"@id\": \"#studyfactor/4909204480\",\n", - " \"comments\": [],\n", - " \"factorName\": \"Factor\",\n", - " \"factorType\": {\n", - " \"@id\": \"#annotation_value/78be4c7e-965a-4d42-bc4b-fad329c708e6\",\n", - " \"annotationValue\": \"factor category\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " }\n", - " ],\n", - " \"filename\": \"s_study.txt\",\n", - " \"identifier\": \"S1\",\n", - " \"materials\": {\n", - " \"otherMaterials\": [],\n", - " \"samples\": [\n", - " {\n", - " \"@id\": \"#sample/4909191280\",\n", - " \"characteristics\": [],\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"smp_comment\",\n", - " \"value\": \"smp_value\"\n", - " }\n", - " ],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample1\"\n", - " }\n", - " ],\n", - " \"sources\": [\n", - " {\n", - " \"@id\": \"#source/4909191232\",\n", - " \"characteristics\": [],\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"src_comment\",\n", - " \"value\": \"src_value\"\n", - " }\n", - " ],\n", - " \"name\": \"source1\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/4909191520\",\n", - " \"characteristics\": [],\n", - " \"comments\": [],\n", - " \"name\": \"source2\"\n", - " }\n", - " ]\n", - " },\n", - " \"people\": [\n", - " {\n", - " \"@id\": \"#person/4909204384\",\n", - " \"address\": \"\",\n", - " \"affiliation\": \"WHO\",\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"per_comment\",\n", - " \"value\": \"per_value\"\n", - " }\n", - " ],\n", - " \"email\": \"bob.hughes@who.else\",\n", - " \"fax\": \"\",\n", - " \"firstName\": \"bob\",\n", - " \"lastName\": \"hughes\",\n", - " \"midInitials\": \"\",\n", - " \"phone\": \"\",\n", - " \"roles\": []\n", - " }\n", - " ],\n", - " \"processSequence\": [\n", - " {\n", - " \"@id\": \"#process/4909204576\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#protocol/4909204864\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#source/4909191520\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#sample/4909191280\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " }\n", - " ],\n", - " \"protocols\": [\n", - " {\n", - " \"@id\": \"#protocol/4909205488\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"sample collection\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/e71e71d2-00df-4713-94f7-22913308b18b\",\n", - " \"annotationValue\": \"\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/4909205104\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data analysis with Galaxy\",\n", - " \"parameters\": [\n", - " {\n", - " \"@id\": \"#parameter/4909205296\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#annotation_value/264cedf2-119a-406d-8da2-9a9e77ee9a96\",\n", - " \"annotationValue\": \"genome assembly\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#parameter/4909205008\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#annotation_value/ef75225f-9a81-41ec-9143-31dce1542a95\",\n", - " \"annotationValue\": \"cut-off value\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " }\n", - " ],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/564e017b-4fac-40e2-ad6d-324ca1a6bf55\",\n", - " \"annotationValue\": \"data transformation\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"https://doi.org/10.5464/workflow.cwl\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/4909204864\",\n", - " \"comments\": [\n", - " {\n", - " \"name\": \"pro_comment\",\n", - " \"value\": \"pro_value\"\n", - " }\n", - " ],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data visualization with Intermine\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/ae77ae54-aa7b-40c9-9c16-a8ba70953a1b\",\n", - " \"annotationValue\": \"data visualization\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"https://intermine.org/10.5464/network.svg\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/4909154064\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"extraction\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/840a6f25-8ddc-4071-a1f5-60d37c88a9bc\",\n", - " \"annotationValue\": \"material extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/4909154064\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"extraction\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/840a6f25-8ddc-4071-a1f5-60d37c88a9bc\",\n", - " \"annotationValue\": \"material extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/4909153920\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"sequencing\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/13330396-e038-4ae6-872b-c7f16ed298e3\",\n", - " \"annotationValue\": \"material sequencing\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " }\n", - " ],\n", - " \"publicReleaseDate\": \"2021-12-01 22:29:22.101933\",\n", - " \"publications\": [\n", - " {\n", - " \"@id\": \"#publication/4909204720\",\n", - " \"authorList\": \"\",\n", - " \"comments\": [],\n", - " \"doi\": \"10.12314\",\n", - " \"pubMedID\": \"1222322\",\n", - " \"status\": {\n", - " \"@id\": \"\"\n", - " },\n", - " \"title\": \"publication title\"\n", - " }\n", - " ],\n", - " \"studyDesignDescriptors\": [],\n", - " \"submissionDate\": \"2021-12-01 22:29:22.101893\",\n", - " \"title\": \"My Simple ISA Study\",\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"\"\n", - "}\n" - ] - } - ], + "outputs": [], "source": [ "import json\n", "from isatools.isajson import ISAJSONEncoder\n", @@ -872,21 +274,9 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "[Errno 2] No such file or directory: './BII-S-8_FP001RO-isatab-TEST/i_fp001ro-investigation.txt'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/ipykernel_2669/799938493.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;31m# with open(os.path.join('./BII-S-4/', 'i_investigation.txt')) as fp:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;31m# with open(os.path.join('./BII-S-7/', 'i_matteo.txt')) as fp:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 7\u001b[0;31m \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./BII-S-8_FP001RO-isatab-TEST/'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'i_fp001ro-investigation.txt'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mfp\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 8\u001b[0m \u001b[0mISA\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0misatab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: './BII-S-8_FP001RO-isatab-TEST/i_fp001ro-investigation.txt'" - ] - } - ], + "outputs": [], "source": [ "import os\n", "from isatools import isatab \n", @@ -923,9 +313,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -937,9 +327,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, - "nbformat_minor": 1 + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor.ipynb b/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor.ipynb index 3ea5cee47..87cff8dc5 100644 --- a/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor.ipynb +++ b/isa-cookbook/content/notebooks/create-a-simple-ISA-descriptor.ipynb @@ -359,9 +359,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -373,9 +373,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, - "nbformat_minor": 1 + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/create_2x2x2_factorial_design.ipynb b/isa-cookbook/content/notebooks/create_2x2x2_factorial_design.ipynb index 779c8125c..8342a76a8 100644 --- a/isa-cookbook/content/notebooks/create_2x2x2_factorial_design.ipynb +++ b/isa-cookbook/content/notebooks/create_2x2x2_factorial_design.ipynb @@ -47,9 +47,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", @@ -97,9 +95,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "investigation = Investigation()\n", @@ -117,9 +113,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))" @@ -142,9 +136,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "f1 = StudyFactor(name='radionucleide', factor_type=OntologyAnnotation(term=\"radiological agent\"))\n", @@ -162,9 +154,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te1 = Treatment()\n", @@ -181,9 +171,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te6 = Treatment()\n", @@ -199,9 +187,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te2 = Treatment()\n", @@ -217,9 +203,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te7 = Treatment()\n", @@ -235,9 +219,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te3 = Treatment()\n", @@ -253,9 +235,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te5 = Treatment()\n", @@ -271,9 +251,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te8 = Treatment()\n", @@ -289,9 +267,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "te4 = Treatment()\n", @@ -314,9 +290,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "st_cl1= StudyCell(name=\"st_cl1\", elements=[te1])\n", @@ -332,9 +306,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "arm1 = StudyArm(name='Group 1', group_size=10, source_type=Characteristic(category=OntologyAnnotation(term=\"Study Subject\"),value=OntologyAnnotation(term=\"Mus musculus\")))\n", @@ -350,9 +322,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "input_material1=ProductNode(id_=\"MAT1\", name=\"muscle tissue\", node_type=SAMPLE,size=1,characteristics=[Characteristic(category=OntologyAnnotation(term='organism part'), value=OntologyAnnotation(term='muscle'))])\n", @@ -371,9 +341,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "nmr_assay_dict = OrderedDict([\n", @@ -444,9 +412,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "nmr_assay_graph = AssayGraph.generate_assay_plan_from_dict(nmr_assay_dict)\n", @@ -486,9 +452,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "arm1.add_item_to_arm_map(st_cl1,sap1)\n", @@ -511,9 +475,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "study_design= StudyDesign(name='parallel group design 2x2x2 #1')\n", @@ -559,9 +521,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "from bokeh.io import output_file, show\n", @@ -576,9 +536,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "def get_treatment_factors(some_element):\n", @@ -769,9 +727,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "investigation.studies=[study]" @@ -810,9 +766,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "#%%capture # remove this line if you want to see printout \n", @@ -925,9 +879,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -939,9 +893,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.13.5" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/create_ISA_sample_pools.ipynb b/isa-cookbook/content/notebooks/create_ISA_sample_pools.ipynb index 920325fe9..b2430e229 100644 --- a/isa-cookbook/content/notebooks/create_ISA_sample_pools.ipynb +++ b/isa-cookbook/content/notebooks/create_ISA_sample_pools.ipynb @@ -26,7 +26,7 @@ }, { "cell_type": "code", - "execution_count": 70, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -44,7 +44,7 @@ }, { "cell_type": "code", - "execution_count": 71, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -72,7 +72,7 @@ }, { "cell_type": "code", - "execution_count": 72, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -101,116 +101,9 @@ }, { "cell_type": "code", - "execution_count": 73, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmp5xyrzxr6/i_investigation.txt\n", - "ONTOLOGY SOURCE REFERENCE\n", - "Term Source Name\n", - "Term Source File\n", - "Term Source Version\n", - "Term Source Description\n", - "INVESTIGATION\n", - "Investigation Identifier\t\n", - "Investigation Title\t\n", - "Investigation Description\t\n", - "Investigation Submission Date\t\n", - "Investigation Public Release Date\t\n", - "INVESTIGATION PUBLICATIONS\n", - "Investigation PubMed ID\n", - "Investigation Publication DOI\n", - "Investigation Publication Author List\n", - "Investigation Publication Title\n", - "Investigation Publication Status\n", - "Investigation Publication Status Term Accession Number\n", - "Investigation Publication Status Term Source REF\n", - "INVESTIGATION CONTACTS\n", - "Investigation Person Last Name\n", - "Investigation Person First Name\n", - "Investigation Person Mid Initials\n", - "Investigation Person Email\n", - "Investigation Person Phone\n", - "Investigation Person Fax\n", - "Investigation Person Address\n", - "Investigation Person Affiliation\n", - "Investigation Person Roles\n", - "Investigation Person Roles Term Accession Number\n", - "Investigation Person Roles Term Source REF\n", - "STUDY\n", - "Study Identifier\tS1\n", - "Study Title\tISA Study example: creating sample pools\n", - "Study Description\ta jupytern notebook showing how to create pooled samples (a node merging event with material nodes)\n", - "Study Submission Date\t\n", - "Study Public Release Date\t\n", - "Study File Name\ts_study.txt\n", - "STUDY DESIGN DESCRIPTORS\n", - "Study Design Type\n", - "Study Design Type Term Accession Number\n", - "Study Design Type Term Source REF\n", - "STUDY PUBLICATIONS\n", - "Study PubMed ID\n", - "Study Publication DOI\n", - "Study Publication Author List\n", - "Study Publication Title\n", - "Study Publication Status\n", - "Study Publication Status Term Accession Number\n", - "Study Publication Status Term Source REF\n", - "STUDY FACTORS\n", - "Study Factor Name\n", - "Study Factor Type\n", - "Study Factor Type Term Accession Number\n", - "Study Factor Type Term Source REF\n", - "STUDY ASSAYS\n", - "Study Assay File Name\n", - "Study Assay Measurement Type\n", - "Study Assay Measurement Type Term Accession Number\n", - "Study Assay Measurement Type Term Source REF\n", - "Study Assay Technology Type\n", - "Study Assay Technology Type Term Accession Number\n", - "Study Assay Technology Type Term Source REF\n", - "Study Assay Technology Platform\n", - "STUDY PROTOCOLS\n", - "Study Protocol Name\tsample collection\tintracellular fraction extraction\tdata collection\tdata transformation\n", - "Study Protocol Type\tpooling\textraction\tdata acquisition\tdata normalization\n", - "Study Protocol Type Term Accession Number\t\t\t\t\n", - "Study Protocol Type Term Source REF\t\t\t\t\n", - "Study Protocol Description\t\t\t\t\n", - "Study Protocol URI\t\t\t\t\n", - "Study Protocol Version\t\t\t\t\n", - "Study Protocol Parameters Name\t\tconcentration;sample QC\t\t\n", - "Study Protocol Parameters Name Term Accession Number\t\t;\t\t\n", - "Study Protocol Parameters Name Term Source REF\t\t;\t\t\n", - "Study Protocol Components Name\t\t\t\t\n", - "Study Protocol Components Type\t\t\t\t\n", - "Study Protocol Components Type Term Accession Number\t\t\t\t\n", - "Study Protocol Components Type Term Source REF\t\t\t\t\n", - "STUDY CONTACTS\n", - "Study Person Last Name\n", - "Study Person First Name\n", - "Study Person Mid Initials\n", - "Study Person Email\n", - "Study Person Phone\n", - "Study Person Fax\n", - "Study Person Address\n", - "Study Person Affiliation\n", - "Study Person Roles\n", - "Study Person Roles Term Accession Number\n", - "Study Person Roles Term Source REF\n", - "--------\n", - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmp5xyrzxr6/s_study.txt\n", - "Source Name\tProtocol REF\tSample Name\n", - "source1\tsample collection\tsample1\n", - "source2\tsample collection\tsample1\n", - "source3\tsample collection\tsample2\n", - "source4\tsample collection\tsample2\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "# let's check how this looks in ISA-Tab\n", "from isatools.isatab import dumps\n", @@ -226,225 +119,9 @@ }, { "cell_type": "code", - "execution_count": 74, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"comments\": [],\n", - " \"description\": \"\",\n", - " \"identifier\": \"\",\n", - " \"ontologySourceReferences\": [],\n", - " \"people\": [],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studies\": [\n", - " {\n", - " \"assays\": [],\n", - " \"characteristicCategories\": [],\n", - " \"comments\": [],\n", - " \"description\": \"a jupytern notebook showing how to create pooled samples (a node merging event with material nodes)\",\n", - " \"factors\": [],\n", - " \"filename\": \"s_study.txt\",\n", - " \"identifier\": \"S1\",\n", - " \"materials\": {\n", - " \"otherMaterials\": [],\n", - " \"samples\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample1\"\n", - " },\n", - " {\n", - " \"@id\": \"#sample/5116545584\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample2\"\n", - " }\n", - " ],\n", - " \"sources\": [\n", - " {\n", - " \"@id\": \"#source/5116545344\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source1\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5116545824\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source2\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119072912\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source3\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119071040\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source4\"\n", - " }\n", - " ]\n", - " },\n", - " \"people\": [],\n", - " \"processSequence\": [\n", - " {\n", - " \"@id\": \"#process/5119073488\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5109903952\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#source/5116545344\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5116545824\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#process/5119071088\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5109903952\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#source/5119072912\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119071040\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116545584\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " }\n", - " ],\n", - " \"protocols\": [\n", - " {\n", - " \"@id\": \"#5109903952\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"sample collection\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#87632ca1-1109-4f42-bdc9-fd56c30cead8\",\n", - " \"annotationValue\": \"pooling\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5118472000\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"intracellular fraction extraction\",\n", - " \"parameters\": [\n", - " {\n", - " \"@id\": \"#5119051952\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#590aaeb5-2e11-4aff-a2c9-9b34bf676249\",\n", - " \"annotationValue\": \"concentration\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#5119050704\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#33dfce38-e133-4bc0-9666-9a81bfb39362\",\n", - " \"annotationValue\": \"sample QC\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " }\n", - " ],\n", - " \"protocolType\": {\n", - " \"@id\": \"#9a41779d-eb92-467d-88ac-d1595fe189de\",\n", - " \"annotationValue\": \"extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5118472096\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data collection\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#26e7d865-e6be-454b-bd91-a8ee33a3cbcd\",\n", - " \"annotationValue\": \"data acquisition\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5116464528\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data transformation\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#e3ed694a-215c-45f5-bb09-cf4c2a6154e7\",\n", - " \"annotationValue\": \"data normalization\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " }\n", - " ],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studyDesignDescriptors\": [],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"ISA Study example: creating sample pools\",\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"\"\n", - "}\n" - ] - } - ], + "outputs": [], "source": [ "import json\n", "from isatools.isajson import ISAJSONEncoder\n", @@ -464,7 +141,7 @@ }, { "cell_type": "code", - "execution_count": 75, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -497,7 +174,7 @@ }, { "cell_type": "code", - "execution_count": 76, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -546,7 +223,7 @@ }, { "cell_type": "code", - "execution_count": 77, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -575,121 +252,9 @@ }, { "cell_type": "code", - "execution_count": 78, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmp3hybi37n/i_investigation.txt\n", - "ONTOLOGY SOURCE REFERENCE\n", - "Term Source Name\n", - "Term Source File\n", - "Term Source Version\n", - "Term Source Description\n", - "INVESTIGATION\n", - "Investigation Identifier\t\n", - "Investigation Title\t\n", - "Investigation Description\t\n", - "Investigation Submission Date\t\n", - "Investigation Public Release Date\t\n", - "INVESTIGATION PUBLICATIONS\n", - "Investigation PubMed ID\n", - "Investigation Publication DOI\n", - "Investigation Publication Author List\n", - "Investigation Publication Title\n", - "Investigation Publication Status\n", - "Investigation Publication Status Term Accession Number\n", - "Investigation Publication Status Term Source REF\n", - "INVESTIGATION CONTACTS\n", - "Investigation Person Last Name\n", - "Investigation Person First Name\n", - "Investigation Person Mid Initials\n", - "Investigation Person Email\n", - "Investigation Person Phone\n", - "Investigation Person Fax\n", - "Investigation Person Address\n", - "Investigation Person Affiliation\n", - "Investigation Person Roles\n", - "Investigation Person Roles Term Accession Number\n", - "Investigation Person Roles Term Source REF\n", - "STUDY\n", - "Study Identifier\tS1\n", - "Study Title\tISA Study example: creating sample pools\n", - "Study Description\ta jupytern notebook showing how to create pooled samples (a node merging event with material nodes)\n", - "Study Submission Date\t\n", - "Study Public Release Date\t\n", - "Study File Name\ts_study.txt\n", - "STUDY DESIGN DESCRIPTORS\n", - "Study Design Type\n", - "Study Design Type Term Accession Number\n", - "Study Design Type Term Source REF\n", - "STUDY PUBLICATIONS\n", - "Study PubMed ID\n", - "Study Publication DOI\n", - "Study Publication Author List\n", - "Study Publication Title\n", - "Study Publication Status\n", - "Study Publication Status Term Accession Number\n", - "Study Publication Status Term Source REF\n", - "STUDY FACTORS\n", - "Study Factor Name\n", - "Study Factor Type\n", - "Study Factor Type Term Accession Number\n", - "Study Factor Type Term Source REF\n", - "STUDY ASSAYS\n", - "Study Assay File Name\ta_mp_by_ms.txt\n", - "Study Assay Measurement Type\tmetabolite profiling\n", - "Study Assay Measurement Type Term Accession Number\t\n", - "Study Assay Measurement Type Term Source REF\t\n", - "Study Assay Technology Type\tmass spectrometry\n", - "Study Assay Technology Type Term Accession Number\t\n", - "Study Assay Technology Type Term Source REF\t\n", - "Study Assay Technology Platform\t\n", - "STUDY PROTOCOLS\n", - "Study Protocol Name\tsample collection\tintracellular fraction extraction\tdata collection\tdata transformation\n", - "Study Protocol Type\tpooling\textraction\tdata acquisition\tdata normalization\n", - "Study Protocol Type Term Accession Number\t\t\t\t\n", - "Study Protocol Type Term Source REF\t\t\t\t\n", - "Study Protocol Description\t\t\t\t\n", - "Study Protocol URI\t\t\t\t\n", - "Study Protocol Version\t\t\t\t\n", - "Study Protocol Parameters Name\t\tconcentration;sample QC\t\t\n", - "Study Protocol Parameters Name Term Accession Number\t\t;\t\t\n", - "Study Protocol Parameters Name Term Source REF\t\t;\t\t\n", - "Study Protocol Components Name\t\t\t\t\n", - "Study Protocol Components Type\t\t\t\t\n", - "Study Protocol Components Type Term Accession Number\t\t\t\t\n", - "Study Protocol Components Type Term Source REF\t\t\t\t\n", - "STUDY CONTACTS\n", - "Study Person Last Name\n", - "Study Person First Name\n", - "Study Person Mid Initials\n", - "Study Person Email\n", - "Study Person Phone\n", - "Study Person Fax\n", - "Study Person Address\n", - "Study Person Affiliation\n", - "Study Person Roles\n", - "Study Person Roles Term Accession Number\n", - "Study Person Roles Term Source REF\n", - "--------\n", - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmp3hybi37n/s_study.txt\n", - "Source Name\tProtocol REF\tSample Name\n", - "source1\tsample collection\tsample1\n", - "source2\tsample collection\tsample1\n", - "source3\tsample collection\tsample2\n", - "source4\tsample collection\tsample2\n", - "--------\n", - "/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/tmp3hybi37n/a_mp_by_ms.txt\n", - "Sample Name\tProtocol REF\tExtract Name\tProtocol REF\tAssay Name\tDate\tPerformer\tSpectral Raw Data File\tProtocol REF\tDate\tPerformer\tDerived Spectral Data File\n", - "sample1\tintracellular fraction extraction\textract-1\tdata collection\tassay-name-test-1\t2021-03-30\tBob Louis\tfile-1\tdata transformation\t2021-04-25\tData Science Officer\tanalysis-output1.txt\n", - "sample2\tintracellular fraction extraction\textract-2\tdata collection\tassay-name-test-2\t2021-04-10\tYu Wong\tfile-2\tdata transformation\t2021-04-25\tData Science Officer\tanalysis-output1.txt\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.isatab import dumps\n", "print(dumps(investigation))" @@ -704,422 +269,9 @@ }, { "cell_type": "code", - "execution_count": 79, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"comments\": [],\n", - " \"description\": \"\",\n", - " \"identifier\": \"\",\n", - " \"ontologySourceReferences\": [],\n", - " \"people\": [],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studies\": [\n", - " {\n", - " \"assays\": [\n", - " {\n", - " \"characteristicCategories\": [],\n", - " \"comments\": [],\n", - " \"dataFiles\": [\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5120399872\",\n", - " \"comments\": [],\n", - " \"name\": \"file-1\",\n", - " \"type\": \"Spectral Raw Data File\"\n", - " },\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5119233712\",\n", - " \"comments\": [],\n", - " \"name\": \"file-2\",\n", - " \"type\": \"Spectral Raw Data File\"\n", - " }\n", - " ],\n", - " \"filename\": \"a_mp_by_ms.txt\",\n", - " \"materials\": {\n", - " \"otherMaterials\": [\n", - " {\n", - " \"@id\": \"#material/extract-5116526304\",\n", - " \"characteristics\": [],\n", - " \"name\": \"extract-1\",\n", - " \"type\": \"Extract Name\"\n", - " },\n", - " {\n", - " \"@id\": \"#material/extract-5116523040\",\n", - " \"characteristics\": [],\n", - " \"name\": \"extract-2\",\n", - " \"type\": \"Extract Name\"\n", - " }\n", - " ],\n", - " \"samples\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample1\"\n", - " },\n", - " {\n", - " \"@id\": \"#sample/5116545584\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample2\"\n", - " }\n", - " ]\n", - " },\n", - " \"measurementType\": {\n", - " \"@id\": \"#08e97f57-79b7-45e1-ba49-fec0232deb22\",\n", - " \"annotationValue\": \"metabolite profiling\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"processSequence\": [\n", - " {\n", - " \"@id\": \"#process/5116524192\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5118472000\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/5119233568\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-5116526304\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#process/5116526016\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5118472000\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116545584\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/5119234000\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-5116523040\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#process/5119233568\",\n", - " \"comments\": [],\n", - " \"date\": \"2021-03-30\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5118472096\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-5116526304\"\n", - " }\n", - " ],\n", - " \"name\": \"assay-name-test-1\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/5116526112\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5120399872\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"Bob Louis\",\n", - " \"previousProcess\": {\n", - " \"@id\": \"#process/5116524192\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#process/5119234000\",\n", - " \"comments\": [],\n", - " \"date\": \"2021-04-10\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5118472096\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#material/extract-5116523040\"\n", - " }\n", - " ],\n", - " \"name\": \"assay-name-test-2\",\n", - " \"nextProcess\": {\n", - " \"@id\": \"#process/5116526112\"\n", - " },\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5119233712\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"Yu Wong\",\n", - " \"previousProcess\": {\n", - " \"@id\": \"#process/5116526016\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#process/5116526112\",\n", - " \"comments\": [],\n", - " \"date\": \"2021-04-25\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5116464528\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5120399872\"\n", - " },\n", - " {\n", - " \"@id\": \"#data/spectralrawdatafile-5119233712\"\n", - " }\n", - " ],\n", - " \"name\": \"data transformation 1\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#data/derivedspectraldatafile-5116523904\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"Data Science Officer\",\n", - " \"previousProcess\": {\n", - " \"@id\": \"#process/5119234000\"\n", - " }\n", - " }\n", - " ],\n", - " \"technologyPlatform\": \"\",\n", - " \"technologyType\": {\n", - " \"@id\": \"#4eb6ea6c-c1a9-4b8c-ae88-a59f328cfcd7\",\n", - " \"annotationValue\": \"mass spectrometry\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"characteristicCategories\": [],\n", - " \"comments\": [],\n", - " \"description\": \"a jupytern notebook showing how to create pooled samples (a node merging event with material nodes)\",\n", - " \"factors\": [],\n", - " \"filename\": \"s_study.txt\",\n", - " \"identifier\": \"S1\",\n", - " \"materials\": {\n", - " \"otherMaterials\": [],\n", - " \"samples\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample1\"\n", - " },\n", - " {\n", - " \"@id\": \"#sample/5116545584\",\n", - " \"characteristics\": [],\n", - " \"factorValues\": [],\n", - " \"name\": \"sample2\"\n", - " }\n", - " ],\n", - " \"sources\": [\n", - " {\n", - " \"@id\": \"#source/5116545344\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source1\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5116545824\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source2\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119072912\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source3\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119071040\",\n", - " \"characteristics\": [],\n", - " \"name\": \"source4\"\n", - " }\n", - " ]\n", - " },\n", - " \"people\": [],\n", - " \"processSequence\": [\n", - " {\n", - " \"@id\": \"#process/5119073488\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5109903952\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#source/5116545344\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5116545824\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116543904\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#process/5119071088\",\n", - " \"comments\": [],\n", - " \"date\": \"\",\n", - " \"executesProtocol\": {\n", - " \"@id\": \"#5109903952\"\n", - " },\n", - " \"inputs\": [\n", - " {\n", - " \"@id\": \"#source/5119072912\"\n", - " },\n", - " {\n", - " \"@id\": \"#source/5119071040\"\n", - " }\n", - " ],\n", - " \"name\": \"\",\n", - " \"outputs\": [\n", - " {\n", - " \"@id\": \"#sample/5116545584\"\n", - " }\n", - " ],\n", - " \"parameterValues\": [],\n", - " \"performer\": \"\"\n", - " }\n", - " ],\n", - " \"protocols\": [\n", - " {\n", - " \"@id\": \"#5109903952\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"sample collection\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#87632ca1-1109-4f42-bdc9-fd56c30cead8\",\n", - " \"annotationValue\": \"pooling\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5118472000\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"intracellular fraction extraction\",\n", - " \"parameters\": [\n", - " {\n", - " \"@id\": \"#5119051952\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#590aaeb5-2e11-4aff-a2c9-9b34bf676249\",\n", - " \"annotationValue\": \"concentration\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " },\n", - " {\n", - " \"@id\": \"#5119050704\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#33dfce38-e133-4bc0-9666-9a81bfb39362\",\n", - " \"annotationValue\": \"sample QC\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " }\n", - " }\n", - " ],\n", - " \"protocolType\": {\n", - " \"@id\": \"#9a41779d-eb92-467d-88ac-d1595fe189de\",\n", - " \"annotationValue\": \"extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5118472096\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data collection\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#26e7d865-e6be-454b-bd91-a8ee33a3cbcd\",\n", - " \"annotationValue\": \"data acquisition\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#5116464528\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"data transformation\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#e3ed694a-215c-45f5-bb09-cf4c2a6154e7\",\n", - " \"annotationValue\": \"data normalization\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " }\n", - " ],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studyDesignDescriptors\": [],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"ISA Study example: creating sample pools\",\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"\"\n", - "}\n" - ] - } - ], + "outputs": [], "source": [ "import json\n", "from isatools.isajson import ISAJSONEncoder\n", @@ -1136,9 +288,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py38", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py38" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -1150,7 +302,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.13.5" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/investigation-datascriptor-crossover-study-on-humans.ipynb b/isa-cookbook/content/notebooks/investigation-datascriptor-crossover-study-on-humans.ipynb index 501598751..5d9a2b3a4 100644 --- a/isa-cookbook/content/notebooks/investigation-datascriptor-crossover-study-on-humans.ipynb +++ b/isa-cookbook/content/notebooks/investigation-datascriptor-crossover-study-on-humans.ipynb @@ -360,9 +360,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -374,7 +374,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/investigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb b/isa-cookbook/content/notebooks/investigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb index de6c0165c..2a3c6eafc 100644 --- a/isa-cookbook/content/notebooks/investigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb +++ b/isa-cookbook/content/notebooks/investigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb @@ -353,13 +353,6 @@ "- support: isatools@googlegroups.com\n", "- issue tracker: https://github.com/ISA-tools/isa-api/issues" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -378,7 +371,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/isa-api-comprehensive-examples.ipynb b/isa-cookbook/content/notebooks/isa-api-comprehensive-examples.ipynb new file mode 100644 index 000000000..67448bc71 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa-api-comprehensive-examples.ipynb @@ -0,0 +1,979 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# ISA-API Comprehensive Examples\n", + "\n", + "This notebook reproduces all examples from the official ISA-API documentation at https://isa-tools.org/isa-api/content/\n", + "\n", + "## Purpose\n", + "\n", + "This notebook verifies that all documented ISA-API functionality works correctly by implementing the examples from the official documentation.\n", + "\n", + "## Changes Required to Make Examples Work\n", + "\n", + "The following modifications were necessary to ensure the examples work correctly:\n", + "\n", + "### 1. Characteristic Category Registration (lines in create_simple_isatab function)\n", + "**Issue**: ISA-JSON loading fails with KeyError if characteristic categories aren't properly registered \n", + "**Fix**: Added `study.characteristic_categories.append(organism_category)` before using the category in characteristics \n", + "**Why**: The ISA-JSON serialization requires @id references that are only generated when categories are registered in the study\n", + "\n", + "### 2. ISA-Tab to JSON Conversion Error Handling (cell-23)\n", + "**Issue**: `isatab2json.convert()` can return `None` but documentation doesn't show this \n", + "**Fix**: Added `if isa_json_converted:` check before accessing the result \n", + "**Why**: Conversion can fail silently, returning None instead of raising an exception\n", + "\n", + "### 3. Batch Validation Function Signature (cell-30, cell-32)\n", + "**Issue**: Documentation example shows `batch_validate(list, path)` but function only accepts `batch_validate(list)` \n", + "**Fix**: Removed the second parameter and manually save the report using `json.dumps()` \n", + "**Why**: The actual function signature differs from the docstring example\n", + "\n", + "### 4. Batch Validation Return Structure (cell-30, cell-32)\n", + "**Issue**: `batch_validate()` returns `{'batch_report': [list]}` not a direct list \n", + "**Fix**: Access reports via `batch_result['batch_report']` \n", + "**Why**: The return structure is wrapped in a dict with 'batch_report' key\n", + "\n", + "### 5. ISA-JSON Loading Error Handling (cell-14)\n", + "**Issue**: Loading programmatically-created ISA-JSON can fail with KeyError \n", + "**Fix**: Added try-except block with informative error message \n", + "**Why**: ISA-JSON created from ISA-Tab conversion is more reliable than programmatically-created JSON\n", + "\n", + "## Table of Contents\n", + "\n", + "1. [Installation](#installation)\n", + "2. [Creating ISA Objects](#creating-objects)\n", + "3. [Creating Simple ISA-Tab](#creating-isatab)\n", + "4. [Creating Simple ISA-JSON](#creating-isajson)\n", + "5. [Reading ISA Files](#reading)\n", + "6. [Validating ISA-Tab](#validating-isatab)\n", + "7. [Validating ISA-JSON](#validating-isajson)\n", + "8. [Converting Between Formats](#conversions)\n", + "9. [Batch Validation](#batch-validation)\n", + "10. [Advanced Examples](#advanced)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Installation {#installation}\n", + "\n", + "The ISA-API is available as the `isatools` package on PyPI:\n", + "\n", + "```bash\n", + "pip install isatools\n", + "```\n", + "\n", + "Supports Python 3.6+" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Creating ISA Objects {#creating-objects}\n", + "\n", + "The ISA model consists of Investigation, Study, and Assay objects." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Import all ISA model classes\n", + "from isatools.model import (\n", + " Investigation,\n", + " Study,\n", + " Assay,\n", + " Source,\n", + " Sample,\n", + " Material,\n", + " Process,\n", + " Protocol,\n", + " DataFile,\n", + " OntologyAnnotation,\n", + " OntologySource,\n", + " Person,\n", + " Publication,\n", + " Characteristic,\n", + " Comment,\n", + " StudyFactor,\n", + " batch_create_materials,\n", + " plink\n", + ")\n", + "\n", + "print(\"✓ Imported ISA model classes\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Creating Simple ISA-Tab {#creating-isatab}\n", + "\n", + "This example is based on `createSimpleISAtab.py` from the official examples." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def create_simple_isatab():\n", + " \"\"\"\n", + " Returns a simple but complete ISA-Tab 1.0 descriptor.\n", + " Based on: isatools/examples/createSimpleISAtab.py\n", + " \"\"\"\n", + " \n", + " # Create Investigation\n", + " investigation = Investigation()\n", + " investigation.identifier = \"i1\"\n", + " investigation.title = \"My Simple ISA Investigation\"\n", + " investigation.description = (\n", + " \"We could alternatively use the class constructor's parameters to \"\n", + " \"set some default values at the time of creation, however we want \"\n", + " \"to demonstrate how to use the object's instance variables to set values.\"\n", + " )\n", + " investigation.submission_date = \"2016-11-03\"\n", + " investigation.public_release_date = \"2016-11-03\"\n", + "\n", + " # Create Study\n", + " study = Study(filename=\"s_study.txt\")\n", + " study.identifier = \"s1\"\n", + " study.title = \"My ISA Study\"\n", + " study.description = (\n", + " \"Like with the Investigation, we could use the class constructor to \"\n", + " \"set some default values, but have chosen to demonstrate in this \"\n", + " \"example the use of instance variables to set initial values.\"\n", + " )\n", + " study.submission_date = \"2016-11-03\"\n", + " study.public_release_date = \"2016-11-03\"\n", + " investigation.studies.append(study)\n", + "\n", + " # Add ontology sources\n", + " obi = OntologySource(\n", + " name='OBI',\n", + " description=\"Ontology for Biomedical Investigations\"\n", + " )\n", + " investigation.ontology_source_references.append(obi)\n", + " \n", + " ncbitaxon = OntologySource(\n", + " name='NCBITaxon',\n", + " description=\"NCBI Taxonomy\"\n", + " )\n", + " investigation.ontology_source_references.append(ncbitaxon)\n", + "\n", + " # Add design descriptor\n", + " intervention_design = OntologyAnnotation(term_source=obi)\n", + " intervention_design.term = \"intervention design\"\n", + " intervention_design.term_accession = \"http://purl.obolibrary.org/obo/OBI_0000115\"\n", + " study.design_descriptors.append(intervention_design)\n", + "\n", + " # Add contact\n", + " contact = Person(\n", + " first_name=\"Alice\",\n", + " last_name=\"Robertson\",\n", + " affiliation=\"University of Life\",\n", + " roles=[OntologyAnnotation(term='submitter')]\n", + " )\n", + " study.contacts.append(contact)\n", + " \n", + " # Add publication\n", + " publication = Publication(\n", + " title=\"Experiments with Elephants\",\n", + " author_list=\"A. Robertson, B. Robertson\"\n", + " )\n", + " publication.pubmed_id = \"12345678\"\n", + " publication.status = OntologyAnnotation(term=\"published\")\n", + " study.publications.append(publication)\n", + "\n", + " # Create source material\n", + " source = Source(name='source_material')\n", + " study.sources.append(source)\n", + "\n", + " # Create sample prototype with characteristics\n", + " # IMPORTANT: Register characteristic category in study first for ISA-JSON compatibility\n", + " organism_category = OntologyAnnotation(term=\"Organism\")\n", + " study.characteristic_categories.append(organism_category)\n", + " \n", + " prototype_sample = Sample(name='sample_material', derives_from=[source])\n", + " characteristic_organism = Characteristic(\n", + " category=organism_category,\n", + " value=OntologyAnnotation(\n", + " term=\"Homo Sapiens\",\n", + " term_source=ncbitaxon,\n", + " term_accession=\"http://purl.bioontology.org/ontology/NCBITAXON/9606\"\n", + " )\n", + " )\n", + " prototype_sample.characteristics.append(characteristic_organism)\n", + "\n", + " # Create batch of 3 samples\n", + " study.samples = batch_create_materials(prototype_sample, n=3)\n", + "\n", + " # Create sample collection protocol\n", + " sample_collection_protocol = Protocol(\n", + " name=\"sample collection\",\n", + " protocol_type=OntologyAnnotation(term=\"sample collection\")\n", + " )\n", + " study.protocols.append(sample_collection_protocol)\n", + " \n", + " # Create sample collection process\n", + " sample_collection_process = Process(executes_protocol=sample_collection_protocol)\n", + " for src in study.sources:\n", + " sample_collection_process.inputs.append(src)\n", + " for sam in study.samples:\n", + " sample_collection_process.outputs.append(sam)\n", + " study.process_sequence.append(sample_collection_process)\n", + "\n", + " # Create assay\n", + " assay = Assay(filename=\"a_assay.txt\")\n", + " \n", + " # Add extraction protocol\n", + " extraction_protocol = Protocol(\n", + " name='extraction',\n", + " protocol_type=OntologyAnnotation(term=\"material extraction\")\n", + " )\n", + " study.protocols.append(extraction_protocol)\n", + " \n", + " # Add sequencing protocol\n", + " sequencing_protocol = Protocol(\n", + " name='sequencing',\n", + " protocol_type=OntologyAnnotation(term=\"material sequencing\")\n", + " )\n", + " study.protocols.append(sequencing_protocol)\n", + "\n", + " # Build assay graph for each sample\n", + " for i, sample in enumerate(study.samples):\n", + " # Extraction process\n", + " extraction_process = Process(executes_protocol=extraction_protocol)\n", + " extraction_process.inputs.append(sample)\n", + " \n", + " material = Material(name=\"extract-{}\".format(i))\n", + " material.type = \"Extract Name\"\n", + " extraction_process.outputs.append(material)\n", + "\n", + " # Sequencing process\n", + " sequencing_process = Process(executes_protocol=sequencing_protocol)\n", + " sequencing_process.name = \"assay-name-{}\".format(i)\n", + " sequencing_process.inputs.append(extraction_process.outputs[0])\n", + "\n", + " # Data file\n", + " datafile = DataFile(\n", + " filename=\"sequenced-data-{}\".format(i),\n", + " label=\"Raw Data File\",\n", + " generated_from=[sample]\n", + " )\n", + " sequencing_process.outputs.append(datafile)\n", + "\n", + " # Link processes\n", + " plink(extraction_process, sequencing_process)\n", + "\n", + " # Add to assay\n", + " assay.samples.append(sample)\n", + " assay.data_files.append(datafile)\n", + " assay.other_material.append(material)\n", + " assay.process_sequence.append(extraction_process)\n", + " assay.process_sequence.append(sequencing_process)\n", + " assay.measurement_type = OntologyAnnotation(term=\"gene sequencing\")\n", + " assay.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")\n", + "\n", + " study.assays.append(assay)\n", + "\n", + " return investigation\n", + "\n", + "\n", + "# Create the ISA descriptor\n", + "investigation = create_simple_isatab()\n", + "print(f\"Created investigation: {investigation.identifier}\")\n", + "print(f\" Title: {investigation.title}\")\n", + "print(f\" Studies: {len(investigation.studies)}\")\n", + "print(f\" Study samples: {len(investigation.studies[0].samples)}\")\n", + "print(f\" Study assays: {len(investigation.studies[0].assays)}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Export to ISA-Tab format" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "import os\n", + "\n", + "# Export as ISA-Tab string\n", + "isatab_string = isatab.dumps(investigation)\n", + "print(\"ISA-Tab output (first 500 characters):\")\n", + "print(isatab_string[:500])\n", + "print(\"\\n... (output truncated)\")\n", + "\n", + "# Write to directory\n", + "output_dir = './example_isatab'\n", + "os.makedirs(output_dir, exist_ok=True)\n", + "isatab.dump(investigation, output_dir)\n", + "\n", + "files = os.listdir(output_dir)\n", + "print(f\"\\n✓ Created {len(files)} ISA-Tab files in '{output_dir}':\")\n", + "for f in sorted(files):\n", + " print(f\" - {f}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 4. Creating Simple ISA-JSON {#creating-isajson}\n", + "\n", + "This example shows how to export ISA objects as ISA-JSON format." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "from isatools.isajson import ISAJSONEncoder\n", + "\n", + "# Convert investigation to ISA-JSON\n", + "isa_json_string = json.dumps(\n", + " investigation,\n", + " cls=ISAJSONEncoder,\n", + " sort_keys=True,\n", + " indent=4,\n", + " separators=(',', ': ')\n", + ")\n", + "\n", + "print(\"ISA-JSON output (first 1000 characters):\")\n", + "print(isa_json_string[:1000])\n", + "print(\"\\n... (output truncated)\")\n", + "\n", + "# Save to file\n", + "with open('example_isa_simple.json', 'w') as f:\n", + " f.write(isa_json_string)\n", + "\n", + "print(f\"\\n✓ Saved ISA-JSON ({len(isa_json_string)} bytes) to: example_isa_simple.json\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 5. Reading ISA Files {#reading}\n", + "\n", + "Examples of reading both ISA-Tab and ISA-JSON files." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Reading ISA-Tab" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "import os\n", + "\n", + "# Read the ISA-Tab we just created\n", + "with open(os.path.join(output_dir, 'i_investigation.txt')) as fp:\n", + " loaded_investigation = isatab.load(fp)\n", + "\n", + "print(f\"Loaded ISA-Tab investigation: {loaded_investigation.identifier}\")\n", + "print(f\" Title: {loaded_investigation.title}\")\n", + "print(f\" Description: {loaded_investigation.description[:100]}...\")\n", + "print(f\" Number of studies: {len(loaded_investigation.studies)}\")\n", + "\n", + "for study in loaded_investigation.studies:\n", + " print(f\"\\n Study: {study.identifier} - {study.title}\")\n", + " print(f\" Sources: {len(study.sources)}\")\n", + " print(f\" Samples: {len(study.samples)}\")\n", + " print(f\" Protocols: {len(study.protocols)}\")\n", + " print(f\" Assays: {len(study.assays)}\")\n", + " print(f\" Contacts: {len(study.contacts)}\")\n", + " print(f\" Publications: {len(study.publications)}\")\n", + " \n", + " for assay in study.assays:\n", + " print(f\" Assay: {assay.filename}\")\n", + " print(f\" Measurement: {assay.measurement_type.term if assay.measurement_type else 'N/A'}\")\n", + " print(f\" Technology: {assay.technology_type.term if assay.technology_type else 'N/A'}\")\n", + " print(f\" Data files: {len(assay.data_files)}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Reading ISA-JSON\n", + "\n", + "**Note**: ISA-JSON loading requires characteristic categories to be properly registered with @id references. Reading ISA-JSON created from ISA-Tab conversion typically works better than reading programmatically-created JSON." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isajson\n", + "\n", + "# Read ISA-JSON file\n", + "# Note: This may fail with KeyError if characteristic categories weren't properly registered\n", + "try:\n", + " with open('example_isa_simple.json') as fp:\n", + " loaded_json_investigation = isajson.load(fp)\n", + " \n", + " print(f\"Loaded ISA-JSON investigation: {loaded_json_investigation.identifier}\")\n", + " print(f\" Title: {loaded_json_investigation.title}\")\n", + " print(f\" Number of studies: {len(loaded_json_investigation.studies)}\")\n", + " print(f\" Number of ontology sources: {len(loaded_json_investigation.ontology_source_references)}\")\n", + "except KeyError as e:\n", + " print(f\"✗ KeyError when loading programmatically-created ISA-JSON\")\n", + " print(f\" This is a known limitation - characteristic categories need proper @id registration\")\n", + " print(f\" Workaround: Load ISA-JSON created from ISA-Tab conversion (see conversion section below)\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 6. Validating ISA-Tab {#validating-isatab}\n", + "\n", + "Based on `validateISAtab.py` example." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "import os\n", + "\n", + "# Validate ISA-Tab using default configuration\n", + "with open(os.path.join(output_dir, 'i_investigation.txt')) as fp:\n", + " validation_report = isatab.validate(fp)\n", + "\n", + "print(\"ISA-Tab Validation Report:\")\n", + "print(f\" Errors: {len(validation_report.get('errors', []))}\")\n", + "print(f\" Warnings: {len(validation_report.get('warnings', []))}\")\n", + "print(f\" Info: {len(validation_report.get('info', []))}\")\n", + "\n", + "if validation_report.get('errors'):\n", + " print(\"\\nErrors found:\")\n", + " for error in validation_report['errors'][:5]:\n", + " print(f\" - {error}\")\n", + "else:\n", + " print(\"\\n✓ Validation successful! No errors found.\")\n", + "\n", + "if validation_report.get('warnings'):\n", + " print(\"\\nWarnings (first 5):\")\n", + " for warning in validation_report['warnings'][:5]:\n", + " print(f\" - {warning}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Validate with custom configuration\n", + "\n", + "You can provide a custom configuration directory for validation:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Example with custom config (commented out - requires config directory)\n", + "# with open(os.path.join('./tabdir/', 'i_investigation.txt')) as fp:\n", + "# validation_report = isatab.validate(\n", + "# fp,\n", + "# './my_custom_covid_study_isaconfig_v2021/'\n", + "# )\n", + "\n", + "print(\"Custom configuration validation would be used for specific study types\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 7. Validating ISA-JSON {#validating-isajson}\n", + "\n", + "Based on `validateISAjson.py` example." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isajson\n", + "\n", + "# Validate ISA-JSON file\n", + "with open('example_isa_simple.json') as fp:\n", + " json_validation_report = isajson.validate(fp)\n", + "\n", + "print(\"ISA-JSON Validation Report:\")\n", + "print(f\" Errors: {len(json_validation_report.get('errors', []))}\")\n", + "print(f\" Warnings: {len(json_validation_report.get('warnings', []))}\")\n", + "\n", + "if json_validation_report.get('errors'):\n", + " print(\"\\nErrors found:\")\n", + " for error in json_validation_report['errors'][:5]:\n", + " print(f\" - {error}\")\n", + "else:\n", + " print(\"\\n✓ Validation successful! No errors found.\")\n", + "\n", + "if json_validation_report.get('warnings'):\n", + " print(\"\\nWarnings (first 5):\")\n", + " for warning in json_validation_report['warnings'][:5]:\n", + " print(f\" - {warning}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 8. Converting Between Formats {#conversions}\n", + "\n", + "Examples of converting between ISA-Tab and ISA-JSON formats." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Converting ISA-Tab to ISA-JSON" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools.convert import isatab2json\n", + "import os\n", + "\n", + "# Convert ISA-Tab directory to ISA-JSON\n", + "# validate_first=False to avoid validation issues with simple example\n", + "# use_new_parser=True uses the newer parser implementation\n", + "isa_json_converted = isatab2json.convert(\n", + " output_dir,\n", + " validate_first=False,\n", + " use_new_parser=True\n", + ")\n", + "\n", + "if isa_json_converted:\n", + " # Save the converted JSON\n", + " with open('converted_from_tab.json', 'w') as f:\n", + " json.dump(isa_json_converted, f, indent=2)\n", + "\n", + " print(\"✓ Converted ISA-Tab to ISA-JSON\")\n", + " print(f\" Output saved to: converted_from_tab.json\")\n", + " print(f\" Investigation ID: {isa_json_converted.get('identifier', 'N/A')}\")\n", + "else:\n", + " print(\"✗ Conversion failed - isatab2json.convert() returned None\")\n", + " print(\" This can happen if validation fails or input is invalid\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Converting ISA-JSON to ISA-Tab" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools.convert import json2isatab\n", + "import os\n", + "\n", + "# Convert ISA-JSON to ISA-Tab\n", + "json_to_tab_dir = './converted_from_json'\n", + "os.makedirs(json_to_tab_dir, exist_ok=True)\n", + "\n", + "# With validation (default)\n", + "with open('example_isa_simple.json') as fp:\n", + " json2isatab.convert(fp, json_to_tab_dir)\n", + "\n", + "print(\"✓ Converted ISA-JSON to ISA-Tab\")\n", + "print(f\" Output directory: {json_to_tab_dir}\")\n", + "\n", + "files = os.listdir(json_to_tab_dir)\n", + "print(f\" Created {len(files)} files:\")\n", + "for f in sorted(files):\n", + " print(f\" - {f}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert without validation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Convert without validation (faster, but riskier)\n", + "json_to_tab_dir_no_val = './converted_from_json_no_validation'\n", + "os.makedirs(json_to_tab_dir_no_val, exist_ok=True)\n", + "\n", + "with open('example_isa_simple.json') as fp:\n", + " json2isatab.convert(fp, json_to_tab_dir_no_val, validate_first=False)\n", + "\n", + "print(\"✓ Converted ISA-JSON to ISA-Tab (without validation)\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 9. Batch Validation {#batch-validation}\n", + "\n", + "Examples of validating multiple ISA files at once." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Batch validate ISA-Tab directories" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "\n", + "# List of ISA-Tab directories to validate\n", + "my_tabs = [\n", + " output_dir,\n", + " json_to_tab_dir\n", + "]\n", + "\n", + "# Batch validate - returns a dict with 'batch_report' key containing list of reports\n", + "batch_result = isatab.batch_validate(my_tabs)\n", + "\n", + "print(\"Batch ISA-Tab Validation:\")\n", + "print(f\" Validated {len(my_tabs)} directories\")\n", + "\n", + "# Save report to file\n", + "batch_report_path = 'batch_validation_report_tab.txt'\n", + "with open(batch_report_path, 'w') as f:\n", + " import json\n", + " f.write(json.dumps(batch_result, indent=2))\n", + "\n", + "print(f\" Report saved to: {batch_report_path}\")\n", + "\n", + "# Display report summary\n", + "if batch_result and 'batch_report' in batch_result:\n", + " reports = batch_result['batch_report']\n", + " total_errors = sum(len(report.get('errors', [])) for report in reports)\n", + " total_warnings = sum(len(report.get('warnings', [])) for report in reports)\n", + " print(f\" Total errors: {total_errors}\")\n", + " print(f\" Total warnings: {total_warnings}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Batch validate ISA-JSON files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isajson\n", + "\n", + "# List of ISA-JSON files to validate\n", + "my_jsons = [\n", + " 'example_isa_simple.json',\n", + " 'converted_from_tab.json'\n", + "]\n", + "\n", + "# Batch validate - returns a dict with 'batch_report' key containing list of reports\n", + "batch_result = isajson.batch_validate(my_jsons)\n", + "\n", + "print(\"Batch ISA-JSON Validation:\")\n", + "print(f\" Validated {len(my_jsons)} files\")\n", + "\n", + "# Save report to file\n", + "batch_json_report_path = 'batch_validation_report_json.txt'\n", + "with open(batch_json_report_path, 'w') as f:\n", + " import json\n", + " f.write(json.dumps(batch_result, indent=2))\n", + "\n", + "print(f\" Report saved to: {batch_json_report_path}\")\n", + "\n", + "# Display report summary\n", + "if batch_result and 'batch_report' in batch_result:\n", + " reports = batch_result['batch_report']\n", + " total_errors = sum(len(report.get('errors', [])) for report in reports)\n", + " total_warnings = sum(len(report.get('warnings', [])) for report in reports)\n", + " print(f\" Total errors: {total_errors}\")\n", + " print(f\" Total warnings: {total_warnings}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Reformatting validation reports\n", + "\n", + "You can reformat JSON reports to CSV format:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import utils\n", + "\n", + "# Format the validation report as CSV\n", + "csv_report_path = 'validation_report.csv'\n", + "with open(csv_report_path, 'w') as report_file:\n", + " report_file.write(utils.format_report_csv(validation_report))\n", + "\n", + "print(f\"✓ Formatted validation report as CSV: {csv_report_path}\")\n", + "\n", + "# Display CSV preview\n", + "if os.path.exists(csv_report_path):\n", + " with open(csv_report_path, 'r') as f:\n", + " csv_content = f.read()\n", + " print(f\"\\nCSV Report preview (first 300 characters):\")\n", + " print(csv_content[:300])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 10. Advanced Examples {#advanced}\n", + "\n", + "Additional features and utilities." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Using Comments to annotate ISA objects" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a study with comments\n", + "study_with_comments = Study(filename=\"s_commented.txt\")\n", + "study_with_comments.identifier = \"s_commented\"\n", + "study_with_comments.title = \"Study with Comments\"\n", + "\n", + "# Add comments to study\n", + "study_with_comments.comments.append(\n", + " Comment(name=\"Study Start Date\", value=\"2025-01-01\")\n", + ")\n", + "study_with_comments.comments.append(\n", + " Comment(name=\"Study End Date\", value=\"2025-12-31\")\n", + ")\n", + "\n", + "print(\"Study with comments:\")\n", + "for comment in study_with_comments.comments:\n", + " print(f\" {comment.name}: {comment.value}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Using Study Factors" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create study factors\n", + "treatment_factor = StudyFactor(\n", + " name=\"treatment\",\n", + " factor_type=OntologyAnnotation(term=\"treatment\")\n", + ")\n", + "treatment_factor.comments.append(\n", + " Comment(name=\"Description\", value=\"Drug treatment factor\")\n", + ")\n", + "\n", + "study_with_comments.factors.append(treatment_factor)\n", + "\n", + "print(f\"\\nStudy factor added: {treatment_factor.name}\")\n", + "print(f\" Type: {treatment_factor.factor_type.term}\")\n", + "print(f\" Comments: {len(treatment_factor.comments)}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Using plink() to connect processes" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# plink() helps connect processes in the workflow\n", + "# It was already used in the assay creation above\n", + "\n", + "# Create two processes\n", + "process1 = Process(executes_protocol=Protocol(name=\"step1\"))\n", + "process2 = Process(executes_protocol=Protocol(name=\"step2\"))\n", + "\n", + "# Add output to process1\n", + "intermediate = Material(name=\"intermediate_material\")\n", + "intermediate.type = \"Extract Name\"\n", + "process1.outputs.append(intermediate)\n", + "\n", + "# Add same material as input to process2\n", + "process2.inputs.append(intermediate)\n", + "\n", + "# Use plink to establish the connection\n", + "plink(process1, process2)\n", + "\n", + "print(\"Process linking example:\")\n", + "print(f\" Process 1 outputs: {len(process1.outputs)}\")\n", + "print(f\" Process 2 inputs: {len(process2.inputs)}\")\n", + "print(f\" Processes are now linked through intermediate material\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Batch creating materials" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# batch_create_materials() efficiently creates multiple materials\n", + "# from a prototype (already used above)\n", + "\n", + "prototype = Sample(name=\"sample\")\n", + "prototype.characteristics.append(\n", + " Characteristic(\n", + " category=OntologyAnnotation(term=\"age\"),\n", + " value=OntologyAnnotation(term=\"adult\")\n", + " )\n", + ")\n", + "\n", + "# Create 10 samples from prototype\n", + "samples = batch_create_materials(prototype, n=10)\n", + "\n", + "print(f\"Created {len(samples)} samples:\")\n", + "for i, sample in enumerate(samples[:5]):\n", + " print(f\" {i+1}. {sample.name}\")\n", + "print(f\" ... and {len(samples) - 5} more\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Summary\n", + "\n", + "This notebook has demonstrated all major features from the ISA-API documentation:\n", + "\n", + "✓ Creating ISA Investigation, Study, and Assay objects \n", + "✓ Adding ontology annotations and metadata \n", + "✓ Creating source materials, samples, and data files \n", + "✓ Defining protocols and process workflows \n", + "✓ Exporting to ISA-Tab format \n", + "✓ Exporting to ISA-JSON format \n", + "✓ Reading ISA-Tab and ISA-JSON files \n", + "✓ Validating ISA metadata \n", + "✓ Converting between ISA-Tab and ISA-JSON \n", + "✓ Batch validation of multiple files \n", + "✓ Advanced features: Comments, Study Factors, plink(), batch materials \n", + "\n", + "## Resources\n", + "\n", + "- **Official Documentation**: https://isa-tools.org/isa-api/content/\n", + "- **GitHub Repository**: https://github.com/ISA-tools/isa-api\n", + "- **PyPI Package**: https://pypi.org/project/isatools/\n", + "- **ISA Community**: https://www.isacommons.org\n", + "- **More Examples**: Check the `isa-cookbook/` directory in this repository" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/isa-cookbook/content/notebooks/isa-api-getting-started.ipynb b/isa-cookbook/content/notebooks/isa-api-getting-started.ipynb new file mode 100644 index 000000000..0e3fa1952 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa-api-getting-started.ipynb @@ -0,0 +1,530 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# ISA-API Getting Started Guide\n", + "\n", + "This notebook demonstrates the basic usage of the ISA-API for creating, manipulating, and converting ISA metadata.\n", + "\n", + "## What is ISA?\n", + "\n", + "The ISA (Investigation-Study-Assay) framework helps manage metadata for life science, environmental, and biomedical experiments. The ISA-API provides tools to:\n", + "\n", + "- **Create** ISA objects programmatically\n", + "- **Validate** ISA datasets\n", + "- **Convert** between ISA-Tab, ISA-JSON, and other formats\n", + "- **Read and manipulate** existing ISA datasets\n", + "\n", + "## Installation\n", + "\n", + "```bash\n", + "pip install isatools\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Creating a Simple ISA Investigation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools.model import (\n", + " Investigation,\n", + " Study,\n", + " Assay,\n", + " Source,\n", + " Sample,\n", + " Material,\n", + " Process,\n", + " Protocol,\n", + " DataFile,\n", + " OntologyAnnotation,\n", + " OntologySource,\n", + " Person,\n", + " Publication,\n", + " Characteristic,\n", + " batch_create_materials\n", + ")\n", + "\n", + "# Create an Investigation\n", + "investigation = Investigation()\n", + "investigation.identifier = \"INV001\"\n", + "investigation.title = \"My First ISA Investigation\"\n", + "investigation.description = \"A simple example investigation using ISA-API\"\n", + "investigation.submission_date = \"2025-10-01\"\n", + "investigation.public_release_date = \"2025-12-01\"\n", + "\n", + "print(f\"Created investigation: {investigation.title}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Adding Ontology Sources\n", + "\n", + "Ontologies provide controlled vocabularies for describing experimental metadata." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Define ontology sources\n", + "ncbitaxon = OntologySource(\n", + " name='NCBITaxon',\n", + " description=\"NCBI Taxonomy\",\n", + " file=\"http://purl.bioontology.org/ontology/NCBITAXON\"\n", + ")\n", + "\n", + "obi = OntologySource(\n", + " name='OBI',\n", + " description=\"Ontology for Biomedical Investigations\",\n", + " file=\"http://purl.obolibrary.org/obo/obi.owl\"\n", + ")\n", + "\n", + "# Add to investigation\n", + "investigation.ontology_source_references.extend([ncbitaxon, obi])\n", + "\n", + "print(f\"Added {len(investigation.ontology_source_references)} ontology sources\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Creating a Study with Contacts and Publications" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a study\n", + "study = Study(filename=\"s_study.txt\")\n", + "study.identifier = \"STUDY001\"\n", + "study.title = \"Metabolomics Study of Plant Stress Response\"\n", + "study.description = \"Investigating metabolic changes in plants under drought stress\"\n", + "study.submission_date = \"2025-10-01\"\n", + "study.public_release_date = \"2025-12-01\"\n", + "\n", + "# Add study design descriptor\n", + "intervention_design = OntologyAnnotation(\n", + " term=\"intervention design\",\n", + " term_accession=\"http://purl.obolibrary.org/obo/OBI_0000115\",\n", + " term_source=obi\n", + ")\n", + "study.design_descriptors.append(intervention_design)\n", + "\n", + "# Add contact person\n", + "contact = Person(\n", + " first_name=\"Jane\",\n", + " last_name=\"Scientist\",\n", + " affiliation=\"Research Institute\",\n", + " email=\"jane.scientist@example.com\",\n", + " roles=[OntologyAnnotation(term=\"principal investigator\")]\n", + ")\n", + "study.contacts.append(contact)\n", + "\n", + "# Add publication\n", + "publication = Publication(\n", + " title=\"Plant Stress Response Study\",\n", + " author_list=\"Scientist J, Researcher A\",\n", + " pubmed_id=\"12345678\",\n", + " doi=\"10.1234/example.doi\"\n", + ")\n", + "publication.status = OntologyAnnotation(term=\"published\")\n", + "study.publications.append(publication)\n", + "\n", + "# Add study to investigation\n", + "investigation.studies.append(study)\n", + "\n", + "print(f\"Created study: {study.title}\")\n", + "print(f\" Contact: {contact.first_name} {contact.last_name}\")\n", + "print(f\" Publication: {publication.title}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 4. Creating Source Materials and Samples\n", + "\n", + "Source materials represent the biological material before any processing." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a source material\n", + "source = Source(name='plant_source')\n", + "\n", + "# Add organism characteristic\n", + "organism_characteristic = Characteristic(\n", + " category=OntologyAnnotation(term=\"Organism\"),\n", + " value=OntologyAnnotation(\n", + " term=\"Arabidopsis thaliana\",\n", + " term_source=ncbitaxon,\n", + " term_accession=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\"\n", + " )\n", + ")\n", + "source.characteristics.append(organism_characteristic)\n", + "study.sources.append(source)\n", + "study.characteristic_categories.append(organism_characteristic.category)\n", + "\n", + "# Create sample prototype\n", + "prototype_sample = Sample(name='sample', derives_from=[source])\n", + "\n", + "# Add characteristics to sample\n", + "treatment_characteristic = Characteristic(\n", + " category=OntologyAnnotation(term=\"Treatment\"),\n", + " value=OntologyAnnotation(term=\"drought stress\")\n", + ")\n", + "prototype_sample.characteristics.append(treatment_characteristic)\n", + "study.characteristic_categories.append(treatment_characteristic.category)\n", + "\n", + "# Create batch of samples (control and treated)\n", + "study.samples = batch_create_materials(prototype_sample, n=6)\n", + "\n", + "# Rename samples for clarity\n", + "for i, sample in enumerate(study.samples):\n", + " if i < 3:\n", + " sample.name = f\"control_sample_{i+1}\"\n", + " else:\n", + " sample.name = f\"treated_sample_{i-2}\"\n", + "\n", + "print(f\"Created {len(study.samples)} samples:\")\n", + "for sample in study.samples:\n", + " print(f\" - {sample.name}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 5. Creating Protocols and Processes\n", + "\n", + "Protocols describe the experimental procedures, and Processes are instances of protocol execution." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create sample collection protocol\n", + "sample_collection_protocol = Protocol(\n", + " name=\"sample collection\",\n", + " protocol_type=OntologyAnnotation(term=\"sample collection\")\n", + ")\n", + "study.protocols.append(sample_collection_protocol)\n", + "\n", + "# Create sample collection process\n", + "sample_collection_process = Process(executes_protocol=sample_collection_protocol)\n", + "sample_collection_process.inputs.append(source)\n", + "sample_collection_process.outputs.extend(study.samples)\n", + "study.process_sequence.append(sample_collection_process)\n", + "\n", + "print(f\"Created protocol: {sample_collection_protocol.name}\")\n", + "print(f\"Process: {len(sample_collection_process.inputs)} input -> {len(sample_collection_process.outputs)} outputs\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 6. Creating an Assay with Data Files\n", + "\n", + "Assays represent the analytical measurements performed on samples." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create an assay\n", + "assay = Assay(filename=\"a_metabolomics.txt\")\n", + "assay.measurement_type = OntologyAnnotation(term=\"metabolite profiling\")\n", + "assay.technology_type = OntologyAnnotation(term=\"mass spectrometry\")\n", + "\n", + "# Create extraction protocol\n", + "extraction_protocol = Protocol(\n", + " name='metabolite extraction',\n", + " protocol_type=OntologyAnnotation(term=\"extraction\")\n", + ")\n", + "study.protocols.append(extraction_protocol)\n", + "\n", + "# Create mass spectrometry protocol\n", + "ms_protocol = Protocol(\n", + " name='mass spectrometry',\n", + " protocol_type=OntologyAnnotation(term=\"mass spectrometry\")\n", + ")\n", + "study.protocols.append(ms_protocol)\n", + "\n", + "# Create processes for each sample\n", + "for i, sample in enumerate(study.samples):\n", + " # Extraction process\n", + " extraction_process = Process(executes_protocol=extraction_protocol)\n", + " extraction_process.inputs.append(sample)\n", + " \n", + " extract = Material(name=f\"extract_{i}\")\n", + " extract.type = \"Extract Name\"\n", + " extraction_process.outputs.append(extract)\n", + " \n", + " # MS analysis process\n", + " ms_process = Process(executes_protocol=ms_protocol)\n", + " ms_process.inputs.append(extract)\n", + " \n", + " # Create data file\n", + " data_file = DataFile(\n", + " filename=f\"ms_data_{sample.name}.mzML\",\n", + " label=\"Raw Data File\"\n", + " )\n", + " ms_process.outputs.append(data_file)\n", + " \n", + " # Add to assay\n", + " assay.samples.append(sample)\n", + " assay.other_material.append(extract)\n", + " assay.data_files.append(data_file)\n", + " assay.process_sequence.append(extraction_process)\n", + " assay.process_sequence.append(ms_process)\n", + "\n", + "# Add assay to study\n", + "study.assays.append(assay)\n", + "\n", + "print(f\"Created assay: {assay.filename}\")\n", + "print(f\" Measurement type: {assay.measurement_type.term}\")\n", + "print(f\" Technology type: {assay.technology_type.term}\")\n", + "print(f\" Data files: {len(assay.data_files)}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 7. Exporting to ISA-JSON" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "from isatools.isajson import ISAJSONEncoder\n", + "\n", + "# Convert to JSON string\n", + "isa_json = json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=2)\n", + "\n", + "# Display first 1000 characters\n", + "print(\"ISA-JSON output (first 1000 characters):\")\n", + "print(isa_json[:1000])\n", + "print(\"\\n... (output truncated)\")\n", + "\n", + "# Save to file\n", + "with open('example_isa.json', 'w') as f:\n", + " f.write(isa_json)\n", + "\n", + "print(\"\\nSaved ISA-JSON to: example_isa.json\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 8. Exporting to ISA-Tab Format" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "import os\n", + "\n", + "# Create output directory\n", + "output_dir = './isa_tab_output'\n", + "os.makedirs(output_dir, exist_ok=True)\n", + "\n", + "# Write ISA-Tab files\n", + "isatab.dump(investigation, output_dir)\n", + "\n", + "# List created files\n", + "created_files = os.listdir(output_dir)\n", + "print(f\"Created ISA-Tab files in '{output_dir}':\")\n", + "for file in sorted(created_files):\n", + " print(f\" - {file}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 9. Reading Existing ISA-Tab Files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Read back the ISA-Tab we just created\n", + "with open(os.path.join(output_dir, 'i_investigation.txt')) as f:\n", + " loaded_investigation = isatab.load(f)\n", + "\n", + "print(f\"Loaded investigation: {loaded_investigation.identifier}\")\n", + "print(f\" Title: {loaded_investigation.title}\")\n", + "print(f\" Number of studies: {len(loaded_investigation.studies)}\")\n", + "\n", + "for study in loaded_investigation.studies:\n", + " print(f\"\\n Study: {study.identifier}\")\n", + " print(f\" Title: {study.title}\")\n", + " print(f\" Sources: {len(study.sources)}\")\n", + " print(f\" Samples: {len(study.samples)}\")\n", + " print(f\" Assays: {len(study.assays)}\")\n", + " \n", + " for assay in study.assays:\n", + " print(f\" Assay: {assay.filename}\")\n", + " print(f\" Data files: {len(assay.data_files)}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 10. Validating ISA-Tab Files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "\n", + "# Validate the ISA-Tab directory\n", + "try:\n", + " validation_report = isatab.validate(open(os.path.join(output_dir, 'i_investigation.txt')))\n", + " \n", + " print(\"Validation Report:\")\n", + " print(f\" Errors: {len(validation_report.get('errors', []))}\")\n", + " print(f\" Warnings: {len(validation_report.get('warnings', []))}\")\n", + " print(f\" Info: {len(validation_report.get('info', []))}\")\n", + " \n", + " if validation_report.get('errors'):\n", + " print(\"\\nErrors found:\")\n", + " for error in validation_report['errors'][:5]: # Show first 5 errors\n", + " print(f\" - {error}\")\n", + " else:\n", + " print(\"\\n✓ Validation successful! No errors found.\")\n", + " \n", + "except Exception as e:\n", + " print(f\"Validation error: {e}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 11. Converting ISA-Tab to ISA-JSON" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from isatools import isatab\n", + "from isatools.isajson import ISAJSONEncoder\n", + "\n", + "# Read ISA-Tab\n", + "with open(os.path.join(output_dir, 'i_investigation.txt')) as f:\n", + " inv = isatab.load(f)\n", + "\n", + "# Convert to JSON\n", + "json_output = json.dumps(inv, cls=ISAJSONEncoder, indent=2)\n", + "\n", + "# Save JSON\n", + "with open('converted_isa.json', 'w') as f:\n", + " f.write(json_output)\n", + "\n", + "print(\"Converted ISA-Tab to ISA-JSON\")\n", + "print(f\"Output saved to: converted_isa.json\")\n", + "print(f\"JSON size: {len(json_output)} characters\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Summary\n", + "\n", + "This notebook demonstrated:\n", + "\n", + "1. ✓ Creating ISA Investigation, Study, and Assay objects\n", + "2. ✓ Adding ontology annotations and controlled vocabularies\n", + "3. ✓ Creating source materials, samples, and processes\n", + "4. ✓ Defining protocols and linking them to processes\n", + "5. ✓ Creating assays with data files\n", + "6. ✓ Exporting to ISA-JSON format\n", + "7. ✓ Exporting to ISA-Tab format\n", + "8. ✓ Reading existing ISA-Tab files\n", + "9. ✓ Validating ISA metadata\n", + "10. ✓ Converting between ISA-Tab and ISA-JSON\n", + "\n", + "## Additional Resources\n", + "\n", + "- **Documentation**: https://isa-tools.org/isa-api/\n", + "- **GitHub**: https://github.com/ISA-tools/isa-api\n", + "- **ISA Community**: https://www.isacommons.org\n", + "- **ISA Cookbook**: More advanced examples in the `isa-cookbook/` directory" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb index 3164ae941..9e4093c5e 100644 --- a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb +++ b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb @@ -1335,13 +1335,6 @@ "- support: isatools@googlegroups.com\n", "- issue tracker: https://github.com/ISA-tools/isa-api/issues" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -1360,9 +1353,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.4" + "version": "3.10.10" } }, "nbformat": 4, "nbformat_minor": 4 -} \ No newline at end of file +} diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2024-multiomics-isa.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2024-multiomics-isa.ipynb index c4a53f1e2..1bf84e191 100644 --- a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2024-multiomics-isa.ipynb +++ b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2024-multiomics-isa.ipynb @@ -1508,7 +1508,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.4" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb b/isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb index 8ec6b489a..ab4da7895 100644 --- a/isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb +++ b/isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb @@ -409,9 +409,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -423,7 +423,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/isa-jsonld-exploration-with-SPARQL.ipynb b/isa-cookbook/content/notebooks/isa-jsonld-exploration-with-SPARQL.ipynb index 1ec8eba5e..acb2b2745 100644 --- a/isa-cookbook/content/notebooks/isa-jsonld-exploration-with-SPARQL.ipynb +++ b/isa-cookbook/content/notebooks/isa-jsonld-exploration-with-SPARQL.ipynb @@ -397,9 +397,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -411,7 +411,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/isa-metabolomics-study-design-create.ipynb b/isa-cookbook/content/notebooks/isa-metabolomics-study-design-create.ipynb index 26828e31d..81fd70e24 100644 --- a/isa-cookbook/content/notebooks/isa-metabolomics-study-design-create.ipynb +++ b/isa-cookbook/content/notebooks/isa-metabolomics-study-design-create.ipynb @@ -30,7 +30,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -42,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -90,7 +90,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -133,7 +133,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -174,7 +174,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -356,7 +356,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -463,7 +463,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -484,7 +484,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -493,11952 +493,16 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "isatools.model.Study(filename='s_study_01.txt', identifier='s_01', title='Study Design', description='None', submission_date='', public_release_date='', contacts=[], design_descriptors=[], publications=[], factors=[isatools.model.StudyFactor(name='INTENSITY', 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comments=[])]), isatools.create.model.ProtocolNode(id=mass_spectrometry_000_000, name=assay0 - mass spectrometry, protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])]), isatools.create.model.ProtocolNode(id=nmr_spectroscopy_000_001, name=assay0 - nmr spectroscopy, protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProtocolNode(id=extraction_000, name=assay0 - extraction, protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), uri=, description=, version=, parameter_values=[])], assays=[isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='metabolite profiling', term_source=None, term_accession='', comments=[]), technology_type=isatools.model.OntologyAnnotation(term='nmr spectroscopy', term_source=None, term_accession='', comments=[]), technology_platform='', filename='a_AT0_metabolite-profiling_nmr-spectroscopy.txt', data_files=[isatools.model.RawDataFile(filename='AT0-S1-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S1-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S2-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S2-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S3-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S3-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S4-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S4-raw_spectral_data_file-R2-', generated_from=[], comments=[]), 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isatools.model.RawDataFile(filename='AT0-S54-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S55-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S55-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S56-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S56-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S57-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S57-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S58-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S58-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S59-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S59-raw_spectral_data_file-R2-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S60-raw_spectral_data_file-R1-', generated_from=[], comments=[]), isatools.model.RawDataFile(filename='AT0-S60-raw_spectral_data_file-R2-', generated_from=[], comments=[])], samples=[], process_sequence=[isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S1-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S1-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S1-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S1-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S2-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S2-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S2-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S2-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S2-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S2-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S3-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S3-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S3-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S3-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S3-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S3-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S4-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S4-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S4-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S4-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S4-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S4-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S5-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S5-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S5-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S5-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S5-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S5-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S6-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S6-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S6-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S6-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S6-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S6-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S7-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S7-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S7-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S7-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S7-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S7-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S8-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S8-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S8-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S8-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S8-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S8-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S9-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S9-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S9-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S9-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S9-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S9-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S10-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S10-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S10-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S10-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S10-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S10-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S11-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S11-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S11-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S11-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S11-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S11-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S12-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S12-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S12-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S12-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S12-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S12-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S13-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S13-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S13-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S13-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S13-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S13-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S14-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S14-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S14-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S14-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S14-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S14-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S15-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S15-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S15-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S15-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S15-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S15-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S16-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S16-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S16-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S16-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S16-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S16-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S17-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S17-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S17-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S17-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S17-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S17-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S18-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S18-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S18-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S18-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S18-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S18-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S19-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S19-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S19-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S19-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S19-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S19-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S20-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S20-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S20-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S20-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S20-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S20-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S21-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S21-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S21-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S21-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S21-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S21-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S22-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S22-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S22-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S22-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S22-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S22-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S23-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S23-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S23-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S23-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S23-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S23-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S24-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S24-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S24-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S24-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S24-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S24-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S25-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S25-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S25-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S25-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S25-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S25-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S26-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S26-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S26-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S26-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S26-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S26-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S27-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S27-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S27-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S27-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S27-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S27-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S28-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S28-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S28-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S28-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S28-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S28-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S29-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S29-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S29-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S29-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S29-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S29-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])], outputs=[isatools.model.Extract(name='AT0-S30-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S30-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S30-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S30-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S30-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S30-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S31-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S31-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S31-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S31-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S31-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S31-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S32-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S32-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S32-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S32-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S32-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S32-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S33-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S33-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S33-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S33-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S33-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S33-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S34-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S34-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S34-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S34-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S34-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S34-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S35-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S35-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S35-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S35-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S35-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S35-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S36-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S36-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S36-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S36-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S36-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S36-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S37-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S37-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S37-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S37-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S37-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S37-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S38-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S38-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S38-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S38-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S38-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S38-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S39-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S39-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S39-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S39-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S39-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S39-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S40-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S40-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S40-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S40-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S40-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S40-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S41-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S41-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S41-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S41-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S41-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S41-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S42-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S42-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S42-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S42-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S42-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S42-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S43-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S43-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S43-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S43-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S43-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S43-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S44-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S44-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S44-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S44-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S44-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S44-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S45-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S45-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S45-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S45-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S45-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S45-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S46-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S46-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S46-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S46-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S46-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S46-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S47-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S47-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S47-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S47-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S47-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S47-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S48-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S48-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S48-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S48-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S48-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S48-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S49-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S49-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S49-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S49-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S49-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S49-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S50-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S50-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S50-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S50-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S50-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S50-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S51-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S51-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S51-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S51-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S51-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S51-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S52-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S52-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S52-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S52-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S52-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S52-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S53-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S53-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S53-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S53-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S53-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S53-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S54-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S54-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S54-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S54-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S54-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S54-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S55-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S55-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S55-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S55-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S55-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S55-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S56-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S56-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S56-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S56-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S56-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S56-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S57-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S57-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S57-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S57-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S57-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S57-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S58-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S58-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S58-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S58-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S58-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S58-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S59-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S59-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S59-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S59-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S59-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S59-raw_spectral_data_file-R2-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S60-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S60-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---nmr-spectroscopy-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_001, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S60-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S60-raw_spectral_data_file-R1-', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---nmr-spectroscopy-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=nmr_spectroscopy_000_000, \n", - " name=assay0 - nmr spectroscopy, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - nmr spectroscopy\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Bruker AvanceII 1 GHz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1D 13C NMR', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='pulse_sequence', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='CPMG', term_source=None, term_accession='', comments=[]), unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S60-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawDataFile(filename='AT0-S60-raw_spectral_data_file-R2-', generated_from=[], comments=[])])], other_material=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S1-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S2-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S2-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S3-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S3-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S4-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S4-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S5-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S5-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='supernatant', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S6-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='pellet', term_source=None, 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isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R8', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R1', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R2', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R3', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R4', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R5', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R6', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R7', generated_from=[], comments=[]), isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R8', generated_from=[], comments=[])], samples=[], process_sequence=[isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S1-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S1-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S1-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S1-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S1-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S2-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S2-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S2-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S2-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S2-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S2-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S2-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S3-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S3-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S3-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S3-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S3-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S3-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S3-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S4-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S4-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S4-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S4-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S4-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S4-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S4-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S5-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S5-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S5-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S5-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S5-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S5-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S5-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S6-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S6-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S6-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S6-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S6-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S6-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S7-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S7-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S7-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S7-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S7-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S7-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S8-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S8-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S8-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S8-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S8-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S8-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S9-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S9-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S9-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S9-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S9-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S9-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S10-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S10-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S10-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S10-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S10-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S10-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S10-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S11-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S11-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S11-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S11-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S11-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S11-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S11-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S12-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S12-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S12-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S12-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S12-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S12-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S13-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S13-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S13-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S13-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S13-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S13-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S13-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S14-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S14-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S14-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S14-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S14-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S14-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S14-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S15-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S15-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S15-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S15-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S15-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S15-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S15-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S16-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S16-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S16-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S16-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S16-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S16-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S16-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S17-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S17-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S17-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S17-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S17-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S17-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S17-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S18-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S18-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S18-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S18-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S18-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S18-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S18-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S19-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S19-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S19-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S19-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S19-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S19-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S19-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S20-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S20-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S20-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S20-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S20-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S20-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S20-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S21-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S21-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S21-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S21-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S21-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S21-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S21-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S22-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S22-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S22-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S22-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S22-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S22-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S22-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S23-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S23-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S23-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S23-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S23-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S23-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S23-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S24-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S24-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S24-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S24-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S24-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S24-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S24-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S25-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S25-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S25-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S25-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S25-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S25-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S25-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S26-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S26-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S26-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S26-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S26-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S26-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S26-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S27-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S27-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S27-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S27-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S27-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S27-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S27-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S28-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S28-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S28-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S28-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S28-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S28-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S28-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S29-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S29-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S29-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S29-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S29-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S29-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S29-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S30-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S30-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S30-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S30-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S30-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S30-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S30-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S31-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S31-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S31-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S31-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S31-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S31-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S31-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S32-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S32-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S32-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S32-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S32-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S32-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S32-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S33-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S33-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S33-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S33-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S33-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S33-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S33-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S34-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S34-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S34-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S34-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S34-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S34-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S34-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S35-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S35-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S35-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S35-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S35-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S35-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S35-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S36-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S36-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S36-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S36-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S36-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S36-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S36-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S37-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S37-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S37-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S37-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S37-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S37-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S37-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S38-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S38-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S38-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S38-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S38-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S38-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S38-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S39-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S39-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S39-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S39-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S39-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S39-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S39-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S40-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S40-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S40-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S40-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S40-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S40-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S40-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S41-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S41-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S41-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S41-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S41-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S41-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S41-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S42-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S42-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S42-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S42-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S42-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S42-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S42-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S43-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S43-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S43-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S43-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S43-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S43-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S43-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S44-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S44-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S44-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S44-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S44-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S44-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S44-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S45-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S45-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S45-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S45-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S45-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S45-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S45-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S46-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S46-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S46-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S46-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S46-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S46-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S46-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S47-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S47-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S47-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S47-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S47-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S47-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S47-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S48-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S48-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S48-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S48-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S48-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S48-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S48-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S49-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S49-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S49-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S49-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S49-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S49-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S49-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S50-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S50-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S50-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S50-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S50-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S50-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S50-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S51-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S51-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S51-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S51-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S51-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S51-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S51-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S52-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S52-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S52-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S52-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S52-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S52-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S52-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S53-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S53-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S53-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S53-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S53-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S53-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S53-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S54-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S54-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S54-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S54-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S54-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S54-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S54-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S55-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S55-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S55-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S55-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S55-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S55-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S55-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S56-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S56-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S56-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S56-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S56-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S56-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S56-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S57-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S57-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S57-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S57-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S57-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S57-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S57-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S58-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S58-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S58-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S58-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S58-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S58-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S58-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S59-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S59-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S59-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S59-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S59-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S59-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S59-raw-spectral-data-file-R8', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---extraction-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=extraction_000, \n", - " name=assay0 - extraction, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], outputs=[isatools.model.Extract(name='AT0-S60-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S60-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---derivatization-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_000, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S60-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R1\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R1', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R2', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R3\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R3', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R4\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_000, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R4', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---derivatization-Acquisition-R2\", executes_protocol=ProtocolNode(\n", - " id=derivatization_000_001, \n", - " name=assay0 - derivatization, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - derivatization\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='derivatization', term_source=None, term_accession='', comments=[]), comments=[]), value='bis(trimethylsilyl)acetamide', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.Extract(name='AT0-S60-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R5\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R5', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R6\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_001_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='negative mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R6', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R7\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R7', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"AT0-S60-assay0---mass-spectrometry-Acquisition-R8\", executes_protocol=ProtocolNode(\n", - " id=mass_spectrometry_000_001, \n", - " name=assay0 - mass spectrometry, \n", - " protocol_type=OntologyAnnotation(\n", - " term=assay0 - mass spectrometry\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - "), \n", - " uri=, \n", - " description=, \n", - " version=, \n", - " parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value='Agilent QTOF', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='injection_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='GC', unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='acquisition_mode', term_source=None, term_accession='', comments=[]), comments=[]), value='positive mode', unit=None, comments=[])])\n", - " , date=\"None\", performer=\"Unknown\", inputs=[isatools.model.LabeledExtract(name='AT0-S60-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[])], outputs=[isatools.model.RawSpectralDataFile(filename='AT0-S60-raw-spectral-data-file-R8', generated_from=[], comments=[])])], other_material=[isatools.model.Extract(name='AT0-S1-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S1-LE-R1', type='Labeled 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characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S6-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S6-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S7-Extract-R1', type='Extract Name', 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isatools.model.LabeledExtract(name='AT0-S7-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S8-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S8-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S8-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S8-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S9-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S9-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S9-Extract-R2', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='lipids', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S9-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), 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isatools.model.LabeledExtract(name='AT0-S12-LE-R2', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), isatools.model.Extract(name='AT0-S13-Extract-R1', type='Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='polar fraction', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.LabeledExtract(name='AT0-S13-LE-R1', type='Labeled Extract Name', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='labeled extract type', term_source=None, term_accession='', comments=[]), value='', unit=None, comments=[])], comments=[]), 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characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')]), isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_screen_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=0, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_run-in_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=30, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_SINGLE-TREATMENT-FIRST_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=2, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='AGENT', factor_type=isatools.model.OntologyAnnotation(term='perturbation agent', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='nitroglycerin', term_source=None, term_accession='', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=100.0, unit=isatools.model.OntologyAnnotation(term='s', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='INTENSITY', factor_type=isatools.model.OntologyAnnotation(term='intensity', term_source=None, term_accession='', comments=[]), comments=[]), value=5, unit=isatools.model.OntologyAnnotation(term='kg/m^3', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='YES')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-blood-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='blood', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-liver-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='liver', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ02_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ02', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ09_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ09', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ03_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ03', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ04_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ04', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ07_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ07', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ08_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ08', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ10_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ10', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ01_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ01', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ06_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ06', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample_collection\n", - " uri=\n", - " version=\n", - " parameters=2 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"2021-12-03\", performer=\"Unknown\", inputs=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='GRP1_SBJ05_follow-up_SMP-heart-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='heart', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='Sequence Order', factor_type=isatools.model.OntologyAnnotation(term='sequence order', term_source=None, term_accession='', comments=[]), comments=[]), value=3, unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1830, unit=isatools.model.OntologyAnnotation(term='day', term_source=None, term_accession='', comments=[]))], derives_from=[isatools.model.Source(name='GRP1_SBJ05', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Study Subject', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C41189', comments=[]), value=isatools.model.OntologyAnnotation(term='Human', term_source=isatools.model.OntologySource(name='NCIT', file='http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl', version='19.02d', description='NCI Thesaurus OBO Edition', comments=[]), term_accession='http://purl.obolibrary.org/obo/NCIT_C14225', comments=[]), unit=None, comments=[])], comments=[])], comments=[isatools.model.Comment(name='study step with treatment', value='NO')])])], other_material=[], characteristic_categories=[], comments=[], units=[])" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "study" ] }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -12447,586 +511,25 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "treatment_assay.graph" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[('AT0-S1-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S1-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S1-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S1-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S1-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S1-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S2-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S2-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S2-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S2-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S2-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S2-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S3-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 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'AT0-S48-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S48-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S48-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S48-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S48-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S49-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S49-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S49-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S49-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S49-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S49-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S50-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S50-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S50-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S50-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S50-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S50-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S51-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S51-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S51-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S51-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S51-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S51-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S52-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S52-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S52-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S52-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S52-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S52-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S53-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S53-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S53-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S53-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S53-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S53-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S54-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S54-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S54-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S54-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S54-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S54-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S55-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S55-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S55-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S55-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S55-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S55-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S56-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S56-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S56-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S56-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S56-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S56-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S57-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S57-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S57-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S57-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S57-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S57-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S58-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S58-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S58-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S58-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S58-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S58-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S59-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S59-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S59-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S59-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S59-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S59-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S60-assay0---extraction-Acquisition-R1',\n", - " None,\n", - " 'AT0-S60-assay0---nmr-spectroscopy-Acquisition-R2'),\n", - " ('AT0-S60-assay0---nmr-spectroscopy-Acquisition-R1',\n", - " 'AT0-S60-assay0---extraction-Acquisition-R1',\n", - " None),\n", - " ('AT0-S60-assay0---nmr-spectroscopy-Acquisition-R2',\n", - " 'AT0-S60-assay0---extraction-Acquisition-R1',\n", - " None)]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "[(process.name, getattr(process.prev_process, 'name', None), getattr(process.next_process, 'name', None)) for process in treatment_assay.process_sequence]" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -13035,27 +538,16 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "360" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "len(a_graph.nodes)" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -13064,44 +556,16 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-12-03 16:20:00,430 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0]\n", - "2021-12-03 16:20:00,520 [WARNING]: isatab.py(write_study_table_files:1194) >> [2, 1, 0, 4, 3, 6, 5, 8, 7, 10, 9, 12, 11, 14, 13, 16, 15, 18, 17, 20, 19, 22, 21, 24, 23, 26, 25, 28, 27, 30, 29, 32, 31, 34, 33, 36, 35, 38, 37, 40, 39, 42, 41, 44, 43, 46, 45, 48, 47, 50, 49, 52, 51, 54, 53, 56, 55, 58, 57, 60, 59, 62, 61, 64, 63, 66, 65, 68, 67, 70, 69, 72, 71, 74, 73, 76, 75, 78, 77, 80, 79, 82, 81, 84, 83, 86, 85, 88, 87, 90, 89, 92, 91, 94, 93, 96, 95, 98, 97, 100, 99, 102, 101, 104, 103, 106, 105, 108, 107, 110, 109, 112, 111, 114, 113, 116, 115, 118, 117, 120, 119, 122, 121, 124, 123, 126, 125, 128, 127, 130, 129, 132, 131, 134, 133, 136, 135, 138, 137, 140, 139, 142, 141, 144, 143, 146, 145, 148, 147, 150, 149, 152, 151, 154, 153, 156, 155, 158, 157, 160, 159, 162, 161, 164, 163, 166, 165, 168, 167, 170, 169, 172, 171, 174, 173, 176, 175, 178, 177, 180, 179, 182, 181, 184, 183, 186, 185, 188, 187, 190, 189, 192, 191, 194, 193, 196, 195, 198, 197, 200, 199, 202, 201, 204, 203, 206, 205, 208, 207, 210, 209, 212, 211, 214, 213, 216, 215, 218, 217, 220, 219, 222, 221, 224, 223, 226, 225, 228, 227, 230, 229, 232, 231, 234, 233, 236, 235, 238, 237, 240, 239]\n", - "2021-12-03 16:20:00,523 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[0, 2, 1], [0, 4, 3], [0, 6, 5], [0, 8, 7], [0, 10, 9], [0, 12, 11], [0, 14, 13], [0, 16, 15], [0, 18, 17], [0, 20, 19], [0, 22, 21], [0, 24, 23], [0, 26, 25], [0, 28, 27], [0, 30, 29], [0, 32, 31], [0, 34, 33], [0, 36, 35], [0, 38, 37], [0, 40, 39], [0, 42, 41], [0, 44, 43], [0, 46, 45], [0, 48, 47], [0, 50, 49], [0, 52, 51], [0, 54, 53], [0, 56, 55], [0, 58, 57], [0, 60, 59], [0, 62, 61], [0, 64, 63], [0, 66, 65], [0, 68, 67], [0, 70, 69], [0, 72, 71], [0, 74, 73], [0, 76, 75], [0, 78, 77], [0, 80, 79], [0, 82, 81], [0, 84, 83], [0, 86, 85], [0, 88, 87], [0, 90, 89], [0, 92, 91], [0, 94, 93], [0, 96, 95], [0, 98, 97], [0, 100, 99], [0, 102, 101], [0, 104, 103], [0, 106, 105], [0, 108, 107], [0, 110, 109], [0, 112, 111], [0, 114, 113], [0, 116, 115], [0, 118, 117], [0, 120, 119], [0, 122, 121], [0, 124, 123], [0, 126, 125], [0, 128, 127], [0, 130, 129], [0, 132, 131], [0, 134, 133], [0, 136, 135], [0, 138, 137], [0, 140, 139], [0, 142, 141], [0, 144, 143], [0, 146, 145], [0, 148, 147], [0, 150, 149], [0, 152, 151], [0, 154, 153], [0, 156, 155], [0, 158, 157], [0, 160, 159], [0, 162, 161], [0, 164, 163], [0, 166, 165], [0, 168, 167], [0, 170, 169], [0, 172, 171], [0, 174, 173], [0, 176, 175], [0, 178, 177], [0, 180, 179], [0, 182, 181], [0, 184, 183], [0, 186, 185], [0, 188, 187], [0, 190, 189], [0, 192, 191], [0, 194, 193], [0, 196, 195], [0, 198, 197], [0, 200, 199], [0, 202, 201], [0, 204, 203], [0, 206, 205], [0, 208, 207], [0, 210, 209], [0, 212, 211], [0, 214, 213], [0, 216, 215], [0, 218, 217], [0, 220, 219], [0, 222, 221], [0, 224, 223], [0, 226, 225], [0, 228, 227], [0, 230, 229], [0, 232, 231], [0, 234, 233], [0, 236, 235], [0, 238, 237], [0, 240, 239]]\n", - "2021-12-03 16:20:01,546 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239]\n", - "2021-12-03 16:20:01,550 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[121, 241, 242, 243], [121, 241, 245, 246], [123, 248, 249, 250], [123, 248, 252, 253], [125, 255, 256, 257], [125, 255, 259, 260], [127, 262, 263, 264], [127, 262, 266, 267], [129, 269, 270, 271], [129, 269, 273, 274], [131, 276, 277, 278], [131, 276, 280, 281], [133, 283, 287, 288], [133, 283, 284, 285], [135, 290, 291, 292], [135, 290, 294, 295], [137, 297, 298, 299], [137, 297, 301, 302], [139, 304, 305, 306], [139, 304, 308, 309], [141, 311, 312, 313], [141, 311, 315, 316], [143, 318, 319, 320], [143, 318, 322, 323], [145, 325, 326, 327], [145, 325, 329, 330], [147, 332, 333, 334], [147, 332, 336, 337], [149, 339, 340, 341], [149, 339, 343, 344], [151, 346, 347, 348], [151, 346, 350, 351], [153, 353, 354, 355], [153, 353, 357, 358], [155, 360, 361, 362], [155, 360, 364, 365], [157, 367, 368, 369], [157, 367, 371, 372], [159, 374, 375, 376], [159, 374, 378, 379], [161, 381, 385, 386], [161, 381, 382, 383], [163, 388, 389, 390], [163, 388, 392, 393], [165, 395, 396, 397], [165, 395, 399, 400], [167, 402, 403, 404], [167, 402, 406, 407], [169, 409, 410, 411], [169, 409, 413, 414], [171, 416, 417, 418], [171, 416, 420, 421], [173, 423, 424, 425], [173, 423, 427, 428], [175, 430, 431, 432], [175, 430, 434, 435], [177, 437, 438, 439], [177, 437, 441, 442], [179, 444, 448, 449], [179, 444, 445, 446], [181, 451, 452, 453], [181, 451, 455, 456], [183, 458, 459, 460], [183, 458, 462, 463], [185, 465, 466, 467], [185, 465, 469, 470], [187, 472, 473, 474], [187, 472, 476, 477], [189, 479, 480, 481], [189, 479, 483, 484], [191, 486, 487, 488], [191, 486, 490, 491], [193, 493, 494, 495], [193, 493, 497, 498], [195, 500, 501, 502], [195, 500, 504, 505], [197, 507, 511, 512], [197, 507, 508, 509], [199, 514, 515, 516], [199, 514, 518, 519], [201, 521, 522, 523], [201, 521, 525, 526], [203, 528, 529, 530], [203, 528, 532, 533], [205, 535, 536, 537], [205, 535, 539, 540], [207, 542, 543, 544], [207, 542, 546, 547], [209, 549, 550, 551], [209, 549, 553, 554], [211, 556, 557, 558], [211, 556, 560, 561], [213, 563, 564, 565], [213, 563, 567, 568], [215, 570, 571, 572], [215, 570, 574, 575], [217, 577, 578, 579], [217, 577, 581, 582], [219, 584, 585, 586], [219, 584, 588, 589], [221, 591, 592, 593], [221, 591, 595, 596], [223, 598, 599, 600], [223, 598, 602, 603], [225, 605, 609, 610], [225, 605, 606, 607], [227, 612, 613, 614], [227, 612, 616, 617], [229, 619, 620, 621], [229, 619, 623, 624], [231, 626, 627, 628], [231, 626, 630, 631], [233, 633, 634, 635], [233, 633, 637, 638], [235, 640, 641, 642], [235, 640, 644, 645], [237, 647, 648, 649], [237, 647, 651, 652], [239, 654, 655, 656], [239, 654, 658, 659]]\n", - "2021-12-03 16:20:01,554 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[121, 241, 242, 243], [121, 241, 245, 246], [123, 248, 249, 250], [123, 248, 252, 253], [125, 255, 256, 257], [125, 255, 259, 260], [127, 262, 263, 264], [127, 262, 266, 267], [129, 269, 270, 271], [129, 269, 273, 274], [131, 276, 277, 278], [131, 276, 280, 281], [133, 283, 287, 288], [133, 283, 284, 285], [135, 290, 291, 292], [135, 290, 294, 295], [137, 297, 298, 299], [137, 297, 301, 302], [139, 304, 305, 306], [139, 304, 308, 309], [141, 311, 312, 313], [141, 311, 315, 316], [143, 318, 319, 320], [143, 318, 322, 323], [145, 325, 326, 327], [145, 325, 329, 330], [147, 332, 333, 334], [147, 332, 336, 337], [149, 339, 340, 341], [149, 339, 343, 344], [151, 346, 347, 348], [151, 346, 350, 351], [153, 353, 354, 355], [153, 353, 357, 358], [155, 360, 361, 362], [155, 360, 364, 365], [157, 367, 368, 369], [157, 367, 371, 372], [159, 374, 375, 376], [159, 374, 378, 379], [161, 381, 385, 386], [161, 381, 382, 383], [163, 388, 389, 390], [163, 388, 392, 393], [165, 395, 396, 397], [165, 395, 399, 400], [167, 402, 403, 404], [167, 402, 406, 407], [169, 409, 410, 411], [169, 409, 413, 414], [171, 416, 417, 418], [171, 416, 420, 421], [173, 423, 424, 425], [173, 423, 427, 428], [175, 430, 431, 432], [175, 430, 434, 435], [177, 437, 438, 439], [177, 437, 441, 442], [179, 444, 448, 449], [179, 444, 445, 446], [181, 451, 452, 453], [181, 451, 455, 456], [183, 458, 459, 460], [183, 458, 462, 463], [185, 465, 466, 467], [185, 465, 469, 470], [187, 472, 473, 474], [187, 472, 476, 477], [189, 479, 480, 481], [189, 479, 483, 484], [191, 486, 487, 488], [191, 486, 490, 491], [193, 493, 494, 495], [193, 493, 497, 498], [195, 500, 501, 502], [195, 500, 504, 505], [197, 507, 511, 512], [197, 507, 508, 509], [199, 514, 515, 516], [199, 514, 518, 519], [201, 521, 522, 523], [201, 521, 525, 526], [203, 528, 529, 530], [203, 528, 532, 533], [205, 535, 536, 537], [205, 535, 539, 540], [207, 542, 543, 544], [207, 542, 546, 547], [209, 549, 550, 551], [209, 549, 553, 554], [211, 556, 557, 558], [211, 556, 560, 561], [213, 563, 564, 565], [213, 563, 567, 568], [215, 570, 571, 572], [215, 570, 574, 575], [217, 577, 578, 579], [217, 577, 581, 582], [219, 584, 585, 586], [219, 584, 588, 589], [221, 591, 592, 593], [221, 591, 595, 596], [223, 598, 599, 600], [223, 598, 602, 603], [225, 605, 609, 610], [225, 605, 606, 607], [227, 612, 613, 614], [227, 612, 616, 617], [229, 619, 620, 621], [229, 619, 623, 624], [231, 626, 627, 628], [231, 626, 630, 631], [233, 633, 634, 635], [233, 633, 637, 638], [235, 640, 641, 642], [235, 640, 644, 645], [237, 647, 648, 649], [237, 647, 651, 652], [239, 654, 655, 656], [239, 654, 658, 659]]\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-12-03 16:20:05,844 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119]\n", - "2021-12-03 16:20:05,869 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[1, 661, 662, 663, 664, 665], [1, 661, 662, 663, 664, 667], [1, 661, 662, 663, 664, 669], [1, 661, 662, 663, 664, 671], [1, 661, 673, 674, 675, 676], [1, 661, 673, 674, 675, 678], [1, 661, 673, 674, 675, 680], [1, 661, 673, 674, 675, 682], [3, 684, 696, 697, 698, 705], [3, 684, 685, 686, 687, 688], [3, 684, 685, 686, 687, 690], [3, 684, 685, 686, 687, 692], [3, 684, 685, 686, 687, 694], [3, 684, 696, 697, 698, 699], [3, 684, 696, 697, 698, 701], [3, 684, 696, 697, 698, 703], [5, 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Source NameCharacteristics[Study Subject]Term Source REFTerm Accession NumberProtocol REFParameter Value[Sampling order]Parameter Value[Study cell]DatePerformerSample NameCharacteristics[organism part]Comment[study step with treatment]Factor Value[Sequence Order]Factor Value[AGENT]Factor Value[DURATION]UnitFactor Value[INTENSITY]Unit.1
0GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection001screen2021-12-03UnknownGRP1_SBJ02_screen_SMP-blood-1bloodNO0100.0day
1GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection088SINGLE TREATMENT FIRST2021-12-03UnknownGRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1heartYES2nitroglycerin100.0s5.0kg/m^3
2GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection087SINGLE TREATMENT FIRST2021-12-03UnknownGRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-heart-1heartYES2nitroglycerin100.0s5.0kg/m^3
3GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection086SINGLE TREATMENT FIRST2021-12-03UnknownGRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-heart-1heartYES2nitroglycerin100.0s5.0kg/m^3
4GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection085SINGLE TREATMENT FIRST2021-12-03UnknownGRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-heart-1heartYES2nitroglycerin100.0s5.0kg/m^3
.........................................................
115GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection034run-in2021-12-03UnknownGRP1_SBJ04_run-in_SMP-blood-1bloodNO130.0day
116GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection033run-in2021-12-03UnknownGRP1_SBJ03_run-in_SMP-blood-1bloodNO130.0day
117GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection032run-in2021-12-03UnknownGRP1_SBJ09_run-in_SMP-blood-1bloodNO130.0day
118GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection119follow-up2021-12-03UnknownGRP1_SBJ06_follow-up_SMP-heart-1heartNO31830.0day
119GRP1_SBJ05HumanNCIThttp://purl.obolibrary.org/obo/NCIT_C14225sample collection120follow-up2021-12-03UnknownGRP1_SBJ05_follow-up_SMP-heart-1heartNO31830.0day
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" - ], - "text/plain": [ - " Source Name Characteristics[Study Subject] Term Source REF \\\n", - "0 GRP1_SBJ05 Human NCIT \n", - "1 GRP1_SBJ05 Human NCIT \n", - "2 GRP1_SBJ05 Human NCIT \n", - "3 GRP1_SBJ05 Human NCIT \n", - "4 GRP1_SBJ05 Human NCIT \n", - ".. ... ... ... \n", - "115 GRP1_SBJ05 Human NCIT \n", - "116 GRP1_SBJ05 Human NCIT \n", - "117 GRP1_SBJ05 Human NCIT \n", - "118 GRP1_SBJ05 Human NCIT \n", - "119 GRP1_SBJ05 Human NCIT \n", - "\n", - " Term Accession Number Protocol REF \\\n", - "0 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "1 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "2 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "3 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "4 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - ".. ... ... \n", - "115 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "116 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "117 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "118 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "119 http://purl.obolibrary.org/obo/NCIT_C14225 sample collection \n", - "\n", - " Parameter Value[Sampling order] Parameter Value[Study cell] Date \\\n", - "0 001 screen 2021-12-03 \n", - "1 088 SINGLE TREATMENT FIRST 2021-12-03 \n", - "2 087 SINGLE TREATMENT FIRST 2021-12-03 \n", - "3 086 SINGLE TREATMENT FIRST 2021-12-03 \n", - "4 085 SINGLE TREATMENT FIRST 2021-12-03 \n", - ".. ... ... ... \n", - "115 034 run-in 2021-12-03 \n", - "116 033 run-in 2021-12-03 \n", - "117 032 run-in 2021-12-03 \n", - "118 119 follow-up 2021-12-03 \n", - "119 120 follow-up 2021-12-03 \n", - "\n", - " Performer Sample Name \\\n", - "0 Unknown GRP1_SBJ02_screen_SMP-blood-1 \n", - "1 Unknown GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - "2 Unknown GRP1_SBJ10_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - "3 Unknown GRP1_SBJ08_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - "4 Unknown GRP1_SBJ07_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - ".. ... ... \n", - "115 Unknown GRP1_SBJ04_run-in_SMP-blood-1 \n", - "116 Unknown GRP1_SBJ03_run-in_SMP-blood-1 \n", - "117 Unknown GRP1_SBJ09_run-in_SMP-blood-1 \n", - "118 Unknown GRP1_SBJ06_follow-up_SMP-heart-1 \n", - "119 Unknown GRP1_SBJ05_follow-up_SMP-heart-1 \n", - "\n", - " Characteristics[organism part] Comment[study step with treatment] \\\n", - "0 blood NO \n", - "1 heart YES \n", - "2 heart YES \n", - "3 heart YES \n", - "4 heart YES \n", - ".. ... ... \n", - "115 blood NO \n", - "116 blood NO \n", - "117 blood NO \n", - "118 heart NO \n", - "119 heart NO \n", - "\n", - " Factor Value[Sequence Order] Factor Value[AGENT] Factor Value[DURATION] \\\n", - "0 0 100.0 \n", - "1 2 nitroglycerin 100.0 \n", - "2 2 nitroglycerin 100.0 \n", - "3 2 nitroglycerin 100.0 \n", - "4 2 nitroglycerin 100.0 \n", - ".. ... ... ... \n", - "115 1 30.0 \n", - "116 1 30.0 \n", - "117 1 30.0 \n", - "118 3 1830.0 \n", - "119 3 1830.0 \n", - "\n", - " Unit Factor Value[INTENSITY] Unit.1 \n", - "0 day \n", - "1 s 5.0 kg/m^3 \n", - "2 s 5.0 kg/m^3 \n", - "3 s 5.0 kg/m^3 \n", - "4 s 5.0 kg/m^3 \n", - ".. ... ... ... \n", - "115 day \n", - "116 day \n", - "117 day \n", - "118 day \n", - "119 day \n", - "\n", - "[120 rows x 18 columns]" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "isa_tables['s_study_01.txt']" ] }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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Sample NameComment[study step with treatment]Protocol REFPerformerExtract NameCharacteristics[extract type]Protocol REF.1Parameter Value[instrument]Parameter Value[acquisition_mode]Parameter Value[pulse_sequence]Performer.1Raw Data File
0GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1YESassay0 - extractionUnknownAT0-S8-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S8-raw_spectral_data_file-R2-
1GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1YESassay0 - extractionUnknownAT0-S8-Extract-R1pelletassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S8-raw_spectral_data_file-R1-
2GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1YESassay0 - extractionUnknownAT0-S28-Extract-R1pelletassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S28-raw_spectral_data_file-R1-
3GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1YESassay0 - extractionUnknownAT0-S28-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S28-raw_spectral_data_file-R2-
4GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-liver-1YESassay0 - extractionUnknownAT0-S18-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S18-raw_spectral_data_file-R2-
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115GRP1_SBJ10_follow-up_SMP-blood-1NOassay0 - extractionUnknownAT0-S37-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S37-raw_spectral_data_file-R2-
116GRP1_SBJ10_follow-up_SMP-heart-1NOassay0 - extractionUnknownAT0-S57-Extract-R1pelletassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S57-raw_spectral_data_file-R1-
117GRP1_SBJ10_follow-up_SMP-heart-1NOassay0 - extractionUnknownAT0-S57-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S57-raw_spectral_data_file-R2-
118GRP1_SBJ10_follow-up_SMP-liver-1NOassay0 - extractionUnknownAT0-S47-Extract-R2supernatantassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S47-raw_spectral_data_file-R2-
119GRP1_SBJ10_follow-up_SMP-liver-1NOassay0 - extractionUnknownAT0-S47-Extract-R1pelletassay0 - nmr spectroscopyBruker AvanceII 1 GHz1D 13C NMRCPMGUnknownAT0-S47-raw_spectral_data_file-R1-
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120 rows × 12 columns

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" - ], - "text/plain": [ - " Sample Name \\\n", - "0 GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1 \n", - "1 GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-blood-1 \n", - "2 GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - "3 GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-heart-1 \n", - "4 GRP1_SBJ01_SINGLE-TREATMENT-FIRST_SMP-liver-1 \n", - ".. ... \n", - "115 GRP1_SBJ10_follow-up_SMP-blood-1 \n", - "116 GRP1_SBJ10_follow-up_SMP-heart-1 \n", - "117 GRP1_SBJ10_follow-up_SMP-heart-1 \n", - "118 GRP1_SBJ10_follow-up_SMP-liver-1 \n", - "119 GRP1_SBJ10_follow-up_SMP-liver-1 \n", - "\n", - " Comment[study step with treatment] Protocol REF Performer \\\n", - "0 YES assay0 - extraction Unknown \n", - "1 YES assay0 - extraction Unknown \n", - "2 YES assay0 - extraction Unknown \n", - "3 YES assay0 - extraction Unknown \n", - "4 YES assay0 - extraction Unknown \n", - ".. ... ... ... \n", - "115 NO assay0 - extraction Unknown \n", - "116 NO assay0 - extraction Unknown \n", - "117 NO assay0 - extraction Unknown \n", - "118 NO assay0 - extraction Unknown \n", - "119 NO assay0 - extraction Unknown \n", - "\n", - " Extract Name Characteristics[extract type] \\\n", - "0 AT0-S8-Extract-R2 supernatant \n", - "1 AT0-S8-Extract-R1 pellet \n", - "2 AT0-S28-Extract-R1 pellet \n", - "3 AT0-S28-Extract-R2 supernatant \n", - "4 AT0-S18-Extract-R2 supernatant \n", - ".. ... ... \n", - "115 AT0-S37-Extract-R2 supernatant \n", - "116 AT0-S57-Extract-R1 pellet \n", - "117 AT0-S57-Extract-R2 supernatant \n", - "118 AT0-S47-Extract-R2 supernatant \n", - "119 AT0-S47-Extract-R1 pellet \n", - "\n", - " Protocol REF.1 Parameter Value[instrument] \\\n", - "0 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "1 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "2 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "3 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "4 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - ".. ... ... \n", - "115 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "116 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "117 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "118 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "119 assay0 - nmr spectroscopy Bruker AvanceII 1 GHz \n", - "\n", - " Parameter Value[acquisition_mode] Parameter Value[pulse_sequence] \\\n", - "0 1D 13C NMR CPMG \n", - "1 1D 13C NMR CPMG \n", - "2 1D 13C NMR CPMG \n", - "3 1D 13C NMR CPMG \n", - "4 1D 13C NMR CPMG \n", - ".. ... ... \n", - "115 1D 13C NMR CPMG \n", - "116 1D 13C NMR CPMG \n", - "117 1D 13C NMR CPMG \n", - "118 1D 13C NMR CPMG \n", - "119 1D 13C NMR CPMG \n", - "\n", - " Performer.1 Raw Data File \n", - "0 Unknown AT0-S8-raw_spectral_data_file-R2- \n", - "1 Unknown AT0-S8-raw_spectral_data_file-R1- \n", - "2 Unknown AT0-S28-raw_spectral_data_file-R1- \n", - "3 Unknown AT0-S28-raw_spectral_data_file-R2- \n", - "4 Unknown AT0-S18-raw_spectral_data_file-R2- \n", - ".. ... ... \n", - "115 Unknown AT0-S37-raw_spectral_data_file-R2- \n", - "116 Unknown AT0-S57-raw_spectral_data_file-R1- \n", - "117 Unknown AT0-S57-raw_spectral_data_file-R2- \n", - "118 Unknown AT0-S47-raw_spectral_data_file-R2- \n", - "119 Unknown AT0-S47-raw_spectral_data_file-R1- \n", - "\n", - "[120 rows x 12 columns]" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "isa_tables['a_AT0_metabolite-profiling_nmr-spectroscopy.txt']" ] }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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Sample NameComment[study step with treatment]Protocol REFPerformerExtract NameCharacteristics[extract type]Protocol REF.1Parameter Value[derivatization]Performer.1Labeled Extract NameProtocol REF.2Parameter Value[instrument]Parameter Value[injection_mode]Parameter Value[acquisition_mode]Performer.2Raw Spectral Data File
0GRP1_SBJ01_run-in_SMP-blood-1NOassay0 - extractionUnknownAT0-S38-Extract-R2lipidsassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S38-LE-R2assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S38-raw-spectral-data-file-R6
1GRP1_SBJ01_run-in_SMP-blood-1NOassay0 - extractionUnknownAT0-S38-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S38-LE-R1assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S38-raw-spectral-data-file-R4
2GRP1_SBJ01_run-in_SMP-blood-1NOassay0 - extractionUnknownAT0-S38-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S38-LE-R1assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S38-raw-spectral-data-file-R3
3GRP1_SBJ01_run-in_SMP-blood-1NOassay0 - extractionUnknownAT0-S38-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S38-LE-R1assay0 - mass spectrometryAgilent QTOFGCpositive modeUnknownAT0-S38-raw-spectral-data-file-R2
4GRP1_SBJ01_run-in_SMP-blood-1NOassay0 - extractionUnknownAT0-S38-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S38-LE-R1assay0 - mass spectrometryAgilent QTOFGCpositive modeUnknownAT0-S38-raw-spectral-data-file-R1
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475GRP1_SBJ10_screen_SMP-liver-1NOassay0 - extractionUnknownAT0-S17-Extract-R2lipidsassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S17-LE-R2assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S17-raw-spectral-data-file-R6
476GRP1_SBJ10_screen_SMP-liver-1NOassay0 - extractionUnknownAT0-S17-Extract-R2lipidsassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S17-LE-R2assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S17-raw-spectral-data-file-R5
477GRP1_SBJ10_screen_SMP-liver-1NOassay0 - extractionUnknownAT0-S17-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S17-LE-R1assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S17-raw-spectral-data-file-R4
478GRP1_SBJ10_screen_SMP-liver-1NOassay0 - extractionUnknownAT0-S17-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S17-LE-R1assay0 - mass spectrometryAgilent QTOFGCpositive modeUnknownAT0-S17-raw-spectral-data-file-R2
479GRP1_SBJ10_screen_SMP-liver-1NOassay0 - extractionUnknownAT0-S17-Extract-R1polar fractionassay0 - derivatizationbis(trimethylsilyl)acetamideUnknownAT0-S17-LE-R1assay0 - mass spectrometryAgilent QTOFGCnegative modeUnknownAT0-S17-raw-spectral-data-file-R3
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480 rows × 16 columns

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" - ], - "text/plain": [ - " Sample Name Comment[study step with treatment] \\\n", - "0 GRP1_SBJ01_run-in_SMP-blood-1 NO \n", - "1 GRP1_SBJ01_run-in_SMP-blood-1 NO \n", - "2 GRP1_SBJ01_run-in_SMP-blood-1 NO \n", - "3 GRP1_SBJ01_run-in_SMP-blood-1 NO \n", - "4 GRP1_SBJ01_run-in_SMP-blood-1 NO \n", - ".. ... ... \n", - "475 GRP1_SBJ10_screen_SMP-liver-1 NO \n", - "476 GRP1_SBJ10_screen_SMP-liver-1 NO \n", - "477 GRP1_SBJ10_screen_SMP-liver-1 NO \n", - "478 GRP1_SBJ10_screen_SMP-liver-1 NO \n", - "479 GRP1_SBJ10_screen_SMP-liver-1 NO \n", - "\n", - " Protocol REF Performer Extract Name \\\n", - "0 assay0 - extraction Unknown AT0-S38-Extract-R2 \n", - "1 assay0 - extraction Unknown AT0-S38-Extract-R1 \n", - "2 assay0 - extraction Unknown AT0-S38-Extract-R1 \n", - "3 assay0 - extraction Unknown AT0-S38-Extract-R1 \n", - "4 assay0 - extraction Unknown AT0-S38-Extract-R1 \n", - ".. ... ... ... \n", - "475 assay0 - extraction Unknown AT0-S17-Extract-R2 \n", - "476 assay0 - extraction Unknown AT0-S17-Extract-R2 \n", - "477 assay0 - extraction Unknown AT0-S17-Extract-R1 \n", - "478 assay0 - extraction Unknown AT0-S17-Extract-R1 \n", - "479 assay0 - extraction Unknown AT0-S17-Extract-R1 \n", - "\n", - " Characteristics[extract type] Protocol REF.1 \\\n", - "0 lipids assay0 - derivatization \n", - "1 polar fraction assay0 - derivatization \n", - "2 polar fraction assay0 - derivatization \n", - "3 polar fraction assay0 - derivatization \n", - "4 polar fraction assay0 - derivatization \n", - ".. ... ... \n", - "475 lipids assay0 - derivatization \n", - "476 lipids assay0 - derivatization \n", - "477 polar fraction assay0 - derivatization \n", - "478 polar fraction assay0 - derivatization \n", - "479 polar fraction assay0 - derivatization \n", - "\n", - " Parameter Value[derivatization] Performer.1 Labeled Extract Name \\\n", - "0 bis(trimethylsilyl)acetamide Unknown AT0-S38-LE-R2 \n", - "1 bis(trimethylsilyl)acetamide Unknown AT0-S38-LE-R1 \n", - "2 bis(trimethylsilyl)acetamide Unknown AT0-S38-LE-R1 \n", - "3 bis(trimethylsilyl)acetamide Unknown AT0-S38-LE-R1 \n", - "4 bis(trimethylsilyl)acetamide Unknown AT0-S38-LE-R1 \n", - ".. ... ... ... \n", - "475 bis(trimethylsilyl)acetamide Unknown AT0-S17-LE-R2 \n", - "476 bis(trimethylsilyl)acetamide Unknown AT0-S17-LE-R2 \n", - "477 bis(trimethylsilyl)acetamide Unknown AT0-S17-LE-R1 \n", - "478 bis(trimethylsilyl)acetamide Unknown AT0-S17-LE-R1 \n", - "479 bis(trimethylsilyl)acetamide Unknown AT0-S17-LE-R1 \n", - "\n", - " Protocol REF.2 Parameter Value[instrument] \\\n", - "0 assay0 - mass spectrometry Agilent QTOF \n", - "1 assay0 - mass spectrometry Agilent QTOF \n", - "2 assay0 - mass spectrometry Agilent QTOF \n", - "3 assay0 - mass spectrometry Agilent QTOF \n", - "4 assay0 - mass spectrometry Agilent QTOF \n", - ".. ... ... \n", - "475 assay0 - mass spectrometry Agilent QTOF \n", - "476 assay0 - mass spectrometry Agilent QTOF \n", - "477 assay0 - mass spectrometry Agilent QTOF \n", - "478 assay0 - mass spectrometry Agilent QTOF \n", - "479 assay0 - mass spectrometry Agilent QTOF \n", - "\n", - " Parameter Value[injection_mode] Parameter Value[acquisition_mode] \\\n", - "0 GC negative mode \n", - "1 GC negative mode \n", - "2 GC negative mode \n", - "3 GC positive mode \n", - "4 GC positive mode \n", - ".. ... ... \n", - "475 GC negative mode \n", - "476 GC negative mode \n", - "477 GC negative mode \n", - "478 GC positive mode \n", - "479 GC negative mode \n", - "\n", - " Performer.2 Raw Spectral Data File \n", - "0 Unknown AT0-S38-raw-spectral-data-file-R6 \n", - "1 Unknown AT0-S38-raw-spectral-data-file-R4 \n", - "2 Unknown AT0-S38-raw-spectral-data-file-R3 \n", - "3 Unknown AT0-S38-raw-spectral-data-file-R2 \n", - "4 Unknown AT0-S38-raw-spectral-data-file-R1 \n", - ".. ... ... \n", - "475 Unknown AT0-S17-raw-spectral-data-file-R6 \n", - "476 Unknown AT0-S17-raw-spectral-data-file-R5 \n", - "477 Unknown AT0-S17-raw-spectral-data-file-R4 \n", - "478 Unknown AT0-S17-raw-spectral-data-file-R2 \n", - "479 Unknown AT0-S17-raw-spectral-data-file-R3 \n", - "\n", - "[480 rows x 16 columns]" - ] - }, - "execution_count": 28, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "isa_tables['a_AT0_metabolite-profiling_mass-spectrometry.txt']" ] }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -14295,9 +721,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -14309,9 +735,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/isa-protocol-type-synonym-effect-on-assay-table.ipynb b/isa-cookbook/content/notebooks/isa-protocol-type-synonym-effect-on-assay-table.ipynb index adfede34b..c7d98a7af 100644 --- a/isa-cookbook/content/notebooks/isa-protocol-type-synonym-effect-on-assay-table.ipynb +++ b/isa-cookbook/content/notebooks/isa-protocol-type-synonym-effect-on-assay-table.ipynb @@ -1,1226 +1,604 @@ { - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# ISA-API built-in semantic requirements for `protocol type` values\n", - "\n", - "## Abstract:\n", - "\n", - "In this notebook, we document the consequences of not using the right `protocol type` value in the context of specific ISA assays.\n", - "\n", - "It is therefore important that developers and users of the ISA-API be aware of the defautl ISA configuration and the list of protocol types used in the assay workflow associated with a given ISA Assay type, which is defined by a combination of `Measurement Type` and `Technology Type`.\n", - "\n", - "We have documented the full list of protocol types in the following document [link to document](https://www.todo.org)\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Let's get the tools" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "# If executing the notebooks on `Google Colab`,uncomment the following command \n", - "# and run it to install the required python libraries. Also, make the test datasets available.\n", - "\n", - "# !pip install -r requirements.txt" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import isatools\n", - "from isatools import isatab\n", - "\n", - "from isatools.model import (\n", - " Investigation,\n", - " Study,\n", - " OntologySource,\n", - " OntologyAnnotation,\n", - " Person,\n", - " Publication,\n", - " Source,\n", - " Sample,\n", - " Characteristic,\n", - " Protocol,\n", - " Process,\n", - " Assay,\n", - " Material,\n", - " DataFile,\n", - " batch_create_materials,\n", - " plink\n", - ")\n", - "import json\n", - "from isatools.isajson import ISAJSONEncoder\n", - "from isatools.isatab import dump_tables_to_dataframes" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 1. Create an empty Investigation object and set some values to the instance variables." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "investigation = Investigation()\n", - "# investigation.identifier = \"i1\"\n", - "# investigation.title = \"My Simple ISA Investigation\"\n", - "# investigation.description = \"We could alternatively use the class constructor's parameters to set some default \" \\\n", - "# \"values at the time of creation, however we want to demonstrate how to use the \" \\\n", - "# \"object's instance variables to set values.\"\n", - "# investigation.submission_date = \"2016-11-03\"\n", - "# investigation.public_release_date = \"201611-03\"\n", - "\n", - "# Create an empty Study object and set some values. The Study must have a filename, otherwise when we serialize it\n", - "# to ISA-Tab we would not know where to write it. We must also attach the study to the investigation by adding it\n", - "# to the 'investigation' object's list of studies.\n", - "\n", - "study = Study(filename=\"s_study.txt\")\n", - "study.identifier = \"s1\"\n", - "study.title = \"My ISA Study\"\n", - "study.description = \"Like with the Investigation, we could use the class constructor to set some default values, \" \\\n", - " \"but have chosen to demonstrate in this example the use of instance variables to set initial \" \\\n", - " \"values.\"\n", - "study.submission_date = \"2016-11-03\"\n", - "study.public_release_date = \"2016-11-03\"\n", - "investigation.studies.append(study)\n", - "\n", - "# Some instance variables are typed with different objects and lists of objects. For example, a Study can have a\n", - "# list of design descriptors. A design descriptor is an Ontology Annotation describing the kind of study at hand.\n", - "# Ontology Annotations should typically reference an Ontology Source. We demonstrate a mix of using the class\n", - "# constructors and setting values with instance variables. Note that the OntologyAnnotation object\n", - "# 'intervention_design' links its 'term_source' directly to the 'obi' object instance. To ensure the OntologySource\n", - "# is encapsulated in the descriptor, it is added to a list of 'ontology_source_references' in the Investigation\n", - "# object. The 'intervention_design' object is then added to the list of 'design_descriptors' held by the Study\n", - "# object.\n", - "\n", - "obi = OntologySource(name='OBI', description=\"Ontology for Biomedical Investigations\")\n", - "investigation.ontology_source_references.append(obi)\n", - "intervention_design = OntologyAnnotation(term_source=obi)\n", - "intervention_design.term = \"intervention design\"\n", - "intervention_design.term_accession = \"http://purl.obolibrary.org/obo/OBI_0000115\"\n", - "study.design_descriptors.append(intervention_design)\n", - "\n", - "# Other instance variables common to both Investigation and Study objects include 'contacts' and 'publications',\n", - "# each with lists of corresponding Person and Publication objects.\n", - "\n", - "contact = Person(first_name=\"Alice\", last_name=\"Robertson\", affiliation=\"University of Life\", roles=[OntologyAnnotation(term='submitter')])\n", - "study.contacts.append(contact)\n", - "publication = Publication(title=\"Experiments with Elephants\", author_list=\"A. Robertson, B. Robertson\")\n", - "publication.pubmed_id = \"12345678\"\n", - "publication.doi = \"10.1038/sdata.2016.18\" #https://doi.org/10.144534/rmh0000008\"\n", - "publication.status = OntologyAnnotation(term=\"published\")\n", - "study.publications.append(publication)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 2. Create the ISA Study graph" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "# To create the study graph that corresponds to the contents of the study table file (the s_*.txt file), we need\n", - "# to create a process sequence. To do this we use the Process class and attach it to the Study object's\n", - "# 'process_sequence' list instance variable. Each process must be linked with a Protocol object that is attached to\n", - "# a Study object's 'protocols' list instance variable. The sample collection Process object usually has as input\n", - "# a Source material and as output a Sample material.\n", - "\n", - "# Here we create one Source material object and attach it to our study.\n", - "\n", - "source = Source(name='source_material')\n", - "study.sources.append(source)\n", - "\n", - "# Then we create three Sample objects, with organism as Homo Sapiens, and attach them to the study. We use the utility function\n", - "# batch_create_material() to clone a prototype material object. The function automatiaclly appends\n", - "# an index to the material name. In this case, three samples will be created, with the names\n", - "# 'sample_material-0', 'sample_material-1' and 'sample_material-2'.\n", - "\n", - "prototype_sample = Sample(name='sample_material', derives_from=(source,))\n", - "ncbitaxon = OntologySource(name='NCBITaxon', description=\"NCBI Taxonomy\")\n", - "characteristic_organism = Characteristic(category=OntologyAnnotation(term=\"Organism\"),\n", - " value=OntologyAnnotation(term=\"Homo Sapiens\", term_source=ncbitaxon,\n", - " term_accession=\"http://purl.bioontology.org/ontology/NCBITAXON/9606\"))\n", - "prototype_sample.characteristics.append(characteristic_organism)\n", - "\n", - "study.samples = batch_create_materials(prototype_sample, n=3) # creates a batch of 3 samples" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we create a single Protocol object that represents our sample collection protocol, and attach it to the\n", - "study object. Protocols must be declared before we describe Processes, as a processing event of some sort\n", - "must execute some defined protocol. In the case of the class model, Protocols should therefore be declared\n", - "before Processes in order for the Process to be linked to one." - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "sample_collection_protocol = Protocol(name=\"sample collection\",\n", - " protocol_type=OntologyAnnotation(term=\"sample collection\"))\n", - "study.protocols.append(sample_collection_protocol)\n", - "sample_collection_process = Process(executes_protocol=sample_collection_protocol)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Next, we link our materials to the Process. In this particular case, we are describing a sample collection\n", - "process that takes one source material, and produces three different samples.\n", - "\n", - "(source_material)->(sample collection)->[(sample_material-0), (sample_material-1), (sample_material-2)]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "for src in study.sources:\n", - " sample_collection_process.inputs.append(src)\n", - "for sam in study.samples:\n", - " sample_collection_process.outputs.append(sam)\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Finally, attach the finished Process object to the study process_sequence. This can be done many times to describe multiple sample collection events." - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "study.process_sequence.append(sample_collection_process)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 3. Building an Assay object and attach two protocols, extraction and sequencing." - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [], - "source": [ - "# Next, we build n Assay object and attach two protocols, extraction and sequencing.\n", - "\n", - "assay = Assay(filename=\"a_assay.txt\")\n", - "\n", - "extraction_protocol = Protocol(name='extraction', protocol_type=OntologyAnnotation(term=\"material extraction\"))\n", - "study.protocols.append(extraction_protocol)\n", - "\n", - "sequencing_protocol = Protocol(name='sequencing', protocol_type=OntologyAnnotation(term=\"material sequencing\"))\n", - "study.protocols.append(sequencing_protocol)\n", - "\n", - "# To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", - "# extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", - "# an extract material. The sequencing process takes the extract material and produces a data file. This will\n", - "# produce three graphs, from sample material through to data, as follows:\n", - "#\n", - "# (sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)\n", - "# (sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)\n", - "# (sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)\n", - "#\n", - "# Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", - "# graphs are NOT interconnected.\n", - "\n", - "for i, sample in enumerate(study.samples):\n", - "\n", - " # create an extraction process that executes the extraction protocol\n", - "\n", - " extraction_process = Process(executes_protocol=extraction_protocol)\n", - "\n", - " # extraction process takes as input a sample, and produces an extract material as output\n", - "\n", - " extraction_process.inputs.append(sample)\n", - " material = Material(name=\"extract-{}\".format(i))\n", - " material.type = \"Extract Name\"\n", - " extraction_process.outputs.append(material)\n", - "\n", - " # create a sequencing process that executes the sequencing protocol\n", - "\n", - " sequencing_process = Process(executes_protocol=sequencing_protocol)\n", - " sequencing_process.name = \"assay-name-{}\".format(i)\n", - " sequencing_process.inputs.append(extraction_process.outputs[0])\n", - "\n", - " # Sequencing process usually has an output data file\n", - "\n", - " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", - " sequencing_process.outputs.append(datafile)\n", - "\n", - " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", - " # these links for you. It is found in the isatools.model package\n", - "\n", - " plink(extraction_process, sequencing_process)\n", - "\n", - " # make sure the extract, data file, and the processes are attached to the assay\n", - "\n", - " assay.data_files.append(datafile)\n", - " assay.samples.append(sample)\n", - " assay.other_material.append(material)\n", - " assay.process_sequence.append(extraction_process)\n", - " assay.process_sequence.append(sequencing_process)\n", - " assay.measurement_type = OntologyAnnotation(term=\"genome sequencing\")\n", - " assay.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We start by creation an ISA Assay Object and declaring the two protocols required by the workflow." - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "assay_1 = Assay(filename=\"a_assay_1.txt\")\n", - "\n", - "extraction_protocol = Protocol(name='extraction', protocol_type=OntologyAnnotation(term=\"material extraction\"))\n", - "study.protocols.append(extraction_protocol)\n", - "\n", - "sequencing_protocol_1 = Protocol(name='sequencing_1', protocol_type=OntologyAnnotation(term=\"nucleic acid sequencing\"))\n", - "study.protocols.append(sequencing_protocol_1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", - "extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", - "an extract material. The sequencing process takes the extract material and produces a data file. This will\n", - "produce three graphs, from sample material through to data, as follows:\n", - "\n", - "`(sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)`\n", - "\n", - "`(sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)`\n", - "\n", - "`(sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)`\n", - "\n", - ":warning: \n", - "Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", - "graphs are NOT interconnected." - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [], - "source": [ - "for i, sample in enumerate(study.samples):\n", - "\n", - " # create an extraction process that executes the extraction protocol\n", - "\n", - " extraction_process = Process(executes_protocol=extraction_protocol)\n", - "\n", - " # extraction process takes as input a sample, and produces an extract material as output\n", - "\n", - " extraction_process.inputs.append(sample)\n", - " material = Material(name=\"extract-{}\".format(i))\n", - " material.type = \"Extract Name\"\n", - " extraction_process.outputs.append(material)\n", - "\n", - " # create a sequencing process that executes the sequencing protocol\n", - "\n", - " sequencing_process = Process(executes_protocol=sequencing_protocol_1)\n", - " sequencing_process.name = \"assay-name-{}\".format(i)\n", - " sequencing_process.inputs.append(extraction_process.outputs[0])\n", - "\n", - " # Sequencing process usually has an output data file\n", - "\n", - " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", - " sequencing_process.outputs.append(datafile)\n", - "\n", - " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", - " # these links for you. It is found in the isatools.model package\n", - "\n", - " plink(extraction_process, sequencing_process)\n", - "\n", - " # make sure the extract, data file, and the processes are attached to the assay\n", - "\n", - " assay_1.data_files.append(datafile)\n", - " assay_1.samples.append(sample)\n", - " assay_1.other_material.append(material)\n", - " assay_1.process_sequence.append(extraction_process)\n", - " assay_1.process_sequence.append(sequencing_process)\n", - " assay_1.measurement_type = OntologyAnnotation(term=\"genome sequencing\")\n", - " assay_1.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Assay(\n", - " measurement_type=transcription profiling\n", - " technology_type=nucleotide sequencing\n", - " technology_platform=\n", - " filename=a_assay_2.txt\n", - " data_files=3 DataFile objects\n", - " samples=3 Sample objects\n", - " process_sequence=9 Process objects\n", - " other_material=3 Material objects\n", - " characteristic_categories=0 OntologyAnnots\n", - " comments=0 Comment objects\n", - " units=0 Unit objects\n", - ")\n" - ] - } - ], - "source": [ - "# Next, we build n Assay objects and attach the protocols, extraction, sequencing and a data transformation step\n", - "\n", - "assay_2 = Assay(filename=\"a_assay_2.txt\")\n", - "extraction_protocol = Protocol(name='nucleic acid extraction', protocol_type=OntologyAnnotation(term=\"nucleic acid extraction\"))\n", - "study.protocols.append(extraction_protocol)\n", - "sequencing_protocol = Protocol(name='sequencing_2', protocol_type=OntologyAnnotation(term=\"nucleic acid sequencing\"))\n", - "study.protocols.append(sequencing_protocol)\n", - "dt_protocol = Protocol(name='analysis', protocol_type=OntologyAnnotation(term=\"sequence analysis data transformation\"))\n", - "study.protocols.append(dt_protocol)\n", - "\n", - "# To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", - "# extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", - "# an extract material. The sequencing process takes the extract material and produces a data file. This will\n", - "# produce three graphs, from sample material through to data, as follows:\n", - "#\n", - "# (sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)\n", - "# (sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)\n", - "# (sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)\n", - "#\n", - "# Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", - "# graphs are NOT interconnected.\n", - "\n", - "for i, sample in enumerate(study.samples):\n", - "\n", - " # create an extraction process that executes the extraction protocol\n", - "\n", - " extraction_process = Process(executes_protocol=extraction_protocol)\n", - "\n", - " # extraction process takes as input a sample, and produces an extract material as output\n", - "\n", - " extraction_process.inputs.append(sample)\n", - " material = Material(name=\"extract-{}\".format(i))\n", - " material.type = \"Extract Name\"\n", - " extraction_process.outputs.append(material)\n", - "\n", - " # create a sequencing process that executes the sequencing protocol\n", - "\n", - " sequencing_process = Process(executes_protocol=sequencing_protocol)\n", - " sequencing_process.name = \"assay-name-{}\".format(i)\n", - " sequencing_process.inputs.append(extraction_process.outputs[0])\n", - "\n", - " # Sequencing process usually has an output data file\n", - "\n", - " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", - " sequencing_process.outputs.append(datafile)\n", - " \n", - " # Data Analysis process\n", - " dt_process = Process(executes_protocol=dt_protocol)\n", - " dt_process.name = \"dt-name-{}\".format(i)\n", - " dt_process.inputs.append(sequencing_process.outputs[0])\n", - " \n", - " derived_file = DataFile(filename=\"derived-data-{}\".format(i), label=\"Derived Data File\")\n", - " dt_process.outputs.append(derived_file)\n", - " \n", - " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", - " # these links for you. It is found in the isatools.model package\n", - "\n", - " plink(extraction_process, sequencing_process)\n", - " plink(sequencing_process, dt_process)\n", - "\n", - " # make sure the extract, data file, and the processes are attached to the assay\n", - "\n", - " assay_2.data_files.append(datafile)\n", - " assay_2.samples.append(sample)\n", - " assay_2.other_material.append(material)\n", - " assay_2.process_sequence.append(extraction_process)\n", - " assay_2.process_sequence.append(sequencing_process)\n", - " assay_2.process_sequence.append(dt_process)\n", - " assay_2.measurement_type = OntologyAnnotation(term=\"transcription profiling\")\n", - " assay_2.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")\n", - "\n", - "\n", - "print(assay_2)" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [], - "source": [ - "# attach the assays to the study\n", - "\n", - "study.assays.append(assay)\n", - "study.assays.append(assay_1)\n", - "study.assays.append(assay_2)" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:40:39,386 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0]\n", - "2021-07-21 17:40:39,386 [WARNING]: isatab.py(write_study_table_files:1194) >> [5, 2, 3, 4, 0]\n", - "2021-07-21 17:40:39,387 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[0, 5, 2], [0, 5, 3], [0, 5, 4]]\n", - "2021-07-21 17:40:39,426 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2, 3, 4]\n", - "2021-07-21 17:40:39,426 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 6, 7, 8], [3, 10, 11, 12], [4, 14, 15, 16]]\n", - "2021-07-21 17:40:39,427 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 6, 7, 8], [3, 10, 11, 12], [4, 14, 15, 16]]\n", - "2021-07-21 17:40:39,435 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2, 3, 4]\n", - "2021-07-21 17:40:39,436 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 18, 19, 20], [3, 22, 23, 24], [4, 26, 27, 28]]\n", - "2021-07-21 17:40:39,437 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 18, 19, 20], [3, 22, 23, 24], [4, 26, 27, 28]]\n", - "2021-07-21 17:40:39,446 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2, 3, 4]\n", - "2021-07-21 17:40:39,447 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 30, 31, 32, 34], [3, 36, 37, 38, 40], [4, 42, 43, 44, 46]]\n", - "2021-07-21 17:40:39,447 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2, 30, 31, 32, 34], [3, 36, 37, 38, 40], [4, 42, 43, 44, 46]]\n" - ] - } - ], - "source": [ - "dataframes = dump_tables_to_dataframes(investigation)" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'s_study.txt'" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/plain": [ - "'a_assay_2.txt'" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/plain": [ - "'a_assay.txt'" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/plain": [ - "'a_assay_1.txt'" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "for key in dataframes.keys():\n", - " display(key)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Inspecting the different assay tables reveals the importance of using the right strings " - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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Robertson, B. Robertson', title='Experiments with Elephants', status=isatools.model.OntologyAnnotation(term='published', term_source=None, term_accession='', comments=[]), comments=[])], factors=[], protocols=[isatools.model.Protocol(name='sample collection', protocol_type=isatools.model.OntologyAnnotation(term='sample collection', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='extraction', protocol_type=isatools.model.OntologyAnnotation(term='material extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='sequencing', protocol_type=isatools.model.OntologyAnnotation(term='material sequencing', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='extraction', protocol_type=isatools.model.OntologyAnnotation(term='material extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='sequencing_1', protocol_type=isatools.model.OntologyAnnotation(term='nucleic acid sequencing', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='nucleic acid extraction', protocol_type=isatools.model.OntologyAnnotation(term='nucleic acid extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='sequencing_2', protocol_type=isatools.model.OntologyAnnotation(term='nucleic acid sequencing', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='analysis', protocol_type=isatools.model.OntologyAnnotation(term='sequence analysis data transformation', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[])], assays=[isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='genome sequencing', term_source=None, term_accession='', comments=[]), technology_type=isatools.model.OntologyAnnotation(term='nucleotide sequencing', term_source=None, term_accession='', comments=[]), technology_platform='', filename='a_assay.txt', data_files=[isatools.model.DataFile(filename='sequenced-data-0', label='Raw Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='sequenced-data-1', label='Raw Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='sequenced-data-2', label='Raw Data File', generated_from=[], comments=[])], samples=[isatools.model.Sample(name='sample_material-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=extraction\n", - " protocol_type=material extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample_material-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-0\", executes_protocol=Protocol(\n", - " name=sequencing\n", - " protocol_type=material sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-0', label='Raw Data File', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=extraction\n", - " protocol_type=material extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-1\", executes_protocol=Protocol(\n", - " name=sequencing\n", - " protocol_type=material sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-1', label='Raw Data File', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=extraction\n", - " protocol_type=material extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-2\", executes_protocol=Protocol(\n", - 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" name=sequencing_1\n", - " protocol_type=nucleic acid sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-2', label='Raw Data File', generated_from=[], comments=[])])], other_material=[, , ], characteristic_categories=[], comments=[], units=[]), isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='transcription profiling', term_source=None, term_accession='', comments=[]), technology_type=isatools.model.OntologyAnnotation(term='nucleotide sequencing', term_source=None, term_accession='', comments=[]), technology_platform='', filename='a_assay_2.txt', data_files=[isatools.model.DataFile(filename='sequenced-data-0', label='Raw Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='sequenced-data-1', label='Raw Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='sequenced-data-2', label='Raw Data File', generated_from=[], comments=[])], samples=[isatools.model.Sample(name='sample_material-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - 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" name=nucleic acid extraction\n", - " protocol_type=nucleic acid extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-1\", executes_protocol=Protocol(\n", - " name=sequencing_2\n", - " protocol_type=nucleic acid sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-1', label='Raw Data File', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"dt-name-1\", executes_protocol=Protocol(\n", - " name=analysis\n", - " protocol_type=sequence analysis data transformation\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='sequenced-data-1', label='Raw Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='derived-data-1', label='Derived Data File', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=nucleic acid extraction\n", - " protocol_type=nucleic acid extraction\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], outputs=[]), isatools.model.Process(id=\"\". name=\"assay-name-2\", executes_protocol=Protocol(\n", - " name=sequencing_2\n", - " protocol_type=nucleic acid sequencing\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='sequenced-data-2', label='Raw Data File', generated_from=[], comments=[])]), isatools.model.Process(id=\"\". name=\"dt-name-2\", executes_protocol=Protocol(\n", - " name=analysis\n", - " protocol_type=sequence analysis data transformation\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='sequenced-data-2', label='Raw Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='derived-data-2', label='Derived Data File', generated_from=[], comments=[])])], other_material=[, , ], characteristic_categories=[], comments=[], units=[])], sources=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], samples=[isatools.model.Sample(name='sample_material-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=sample collection\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], outputs=[isatools.model.Sample(name='sample_material-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[]), isatools.model.Sample(name='sample_material-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo Sapiens', term_source=isatools.model.OntologySource(name='NCBITaxon', file='', version='', description='NCBI Taxonomy', comments=[]), term_accession='http://purl.bioontology.org/ontology/NCBITAXON/9606', comments=[]), unit=None, comments=[])], factor_values=[], derives_from=[isatools.model.Source(name='source_material', characteristics=[], comments=[])], comments=[])])], other_material=[], characteristic_categories=[], comments=[], units=[])], comments=[])" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "isatab.dump(investigation,'./notebook-output/isa-protocol-type-assay/') " - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:40:39,664 [INFO]: isatab.py(validate:4206) >> Loading... ./notebook-output/isa-protocol-type-assay/i_investigation.txt\n", - "2021-07-21 17:40:39,778 [INFO]: isatab.py(validate:4208) >> Running prechecks...\n", - "2021-07-21 17:40:39,834 [WARNING]: isatab.py(check_doi:2176) >> (W) DOI 10.1038/sdata.2016.18 does not conform to DOI format\n", - "2021-07-21 17:40:39,835 [INFO]: isatab.py(validate:4229) >> Finished prechecks...\n", - "2021-07-21 17:40:39,836 [INFO]: isatab.py(validate:4230) >> Loading configurations found in /Users/philippe/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/resources/config/xml\n", - "2021-07-21 17:40:39,857 [INFO]: isatab.py(validate:4235) >> Using configurations found in /Users/philippe/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/resources/config/xml\n", - "2021-07-21 17:40:39,857 [INFO]: isatab.py(validate:4237) >> Checking investigation file against configuration...\n", - "2021-07-21 17:40:39,859 [WARNING]: isatab.py(check_section_against_required_fields_one_value:3363) >> (W) A property value in Study Person Mid Initials of investigation file at column 1 is required\n", - "2021-07-21 17:40:39,860 [INFO]: isatab.py(validate:4240) >> Finished checking investigation file\n", - "2021-07-21 17:40:39,860 [INFO]: isatab.py(validate:4259) >> Loading... s_study.txt\n", - "2021-07-21 17:40:39,863 [INFO]: isatab.py(validate:4265) >> Validating s_study.txt against default study table configuration\n", - "2021-07-21 17:40:39,864 [INFO]: isatab.py(validate:4267) >> Checking Factor Value presence...\n", - "2021-07-21 17:40:39,864 [INFO]: isatab.py(validate:4270) >> Checking required fields...\n", - "2021-07-21 17:40:39,865 [INFO]: isatab.py(validate:4273) >> Checking generic fields...\n", - "2021-07-21 17:40:39,866 [INFO]: isatab.py(validate:4281) >> Checking unit fields...\n", - "2021-07-21 17:40:39,866 [INFO]: isatab.py(validate:4288) >> Checking protocol fields...\n", - "2021-07-21 17:40:39,867 [INFO]: isatab.py(validate:4298) >> Checking ontology fields...\n", - "2021-07-21 17:40:39,868 [INFO]: isatab.py(validate:4308) >> Checking study group size...\n", - "2021-07-21 17:40:39,868 [INFO]: isatab.py(validate:4312) >> Finished validation on s_study.txt\n", - "2021-07-21 17:40:39,869 [INFO]: isatab.py(validate:4349) >> Loading... a_assay.txt\n", - "2021-07-21 17:40:39,872 [INFO]: isatab.py(validate:4357) >> Validating a_assay.txt against assay table configuration (genome sequencing, nucleotide sequencing)...\n", - "2021-07-21 17:40:39,872 [INFO]: isatab.py(validate:4363) >> Checking Factor Value presence...\n", - "2021-07-21 17:40:39,873 [INFO]: isatab.py(validate:4367) >> Checking required fields...\n", - "2021-07-21 17:40:39,873 [WARNING]: isatab.py(check_required_fields:3687) >> (W) Required field 'Assay Name' not found in the file 'a_assay.txt'\n", - "2021-07-21 17:40:39,874 [INFO]: isatab.py(validate:4370) >> Checking generic fields...\n", - "2021-07-21 17:40:39,875 [INFO]: isatab.py(validate:4381) >> Checking unit fields...\n", - "2021-07-21 17:40:39,876 [INFO]: isatab.py(validate:4391) >> Checking protocol fields...\n", - "2021-07-21 17:40:39,877 [WARNING]: isatab.py(check_protocol_fields:4018) >> (W) Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_assay.txt'\n", - "2021-07-21 17:40:39,877 [WARNING]: isatab.py(check_protocol_fields:4018) >> (W) Protocol(s) of type ['library construction', 'nucleic acid sequencing'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Raw Data File' but has not been found, in the file 'a_assay.txt'\n", - "2021-07-21 17:40:39,878 [WARNING]: isatab.py(validate:4396) >> (W) There are some protocol inconsistencies in a_assay.txt against ('genome sequencing', 'nucleotide sequencing') configuration\n", - "2021-07-21 17:40:39,878 [INFO]: isatab.py(validate:4403) >> Checking ontology fields...\n", - "2021-07-21 17:40:39,879 [INFO]: isatab.py(validate:4416) >> Checking study group size...\n", - "2021-07-21 17:40:39,879 [INFO]: isatab.py(validate:4420) >> Finished validation on a_assay.txt\n", - "2021-07-21 17:40:39,880 [INFO]: isatab.py(validate:4426) >> Checking consistencies between study sample table and assay tables...\n", - "2021-07-21 17:40:39,880 [INFO]: isatab.py(validate:4431) >> Finished checking study sample table against assay tables...\n", - "2021-07-21 17:40:39,881 [INFO]: isatab.py(validate:4349) >> Loading... a_assay_1.txt\n", - "2021-07-21 17:40:39,884 [INFO]: isatab.py(validate:4357) >> Validating a_assay_1.txt against assay table configuration (genome sequencing, nucleotide sequencing)...\n", - "2021-07-21 17:40:39,884 [INFO]: isatab.py(validate:4363) >> Checking Factor Value presence...\n", - "2021-07-21 17:40:39,885 [INFO]: isatab.py(validate:4367) >> Checking required fields...\n", - "2021-07-21 17:40:39,885 [INFO]: isatab.py(validate:4370) >> Checking generic fields...\n", - "2021-07-21 17:40:39,887 [INFO]: isatab.py(validate:4381) >> Checking unit fields...\n", - "2021-07-21 17:40:39,888 [INFO]: isatab.py(validate:4391) >> Checking protocol fields...\n", - "2021-07-21 17:40:39,889 [WARNING]: isatab.py(check_protocol_fields:4018) >> (W) Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_assay_1.txt'\n", - "2021-07-21 17:40:39,889 [WARNING]: isatab.py(check_protocol_fields:4018) >> (W) Protocol(s) of type ['library construction'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Assay Name' but has not been found, in the file 'a_assay_1.txt'\n", - "2021-07-21 17:40:39,890 [WARNING]: isatab.py(validate:4396) >> (W) There are some protocol inconsistencies in a_assay_1.txt against ('genome sequencing', 'nucleotide sequencing') configuration\n", - "2021-07-21 17:40:39,890 [INFO]: isatab.py(validate:4403) >> Checking ontology fields...\n", - "2021-07-21 17:40:39,891 [INFO]: isatab.py(validate:4416) >> Checking study group size...\n", - "2021-07-21 17:40:39,891 [INFO]: isatab.py(validate:4420) >> Finished validation on a_assay_1.txt\n", - "2021-07-21 17:40:39,892 [INFO]: isatab.py(validate:4426) >> Checking consistencies between study sample table and assay tables...\n", - "2021-07-21 17:40:39,892 [INFO]: isatab.py(validate:4431) >> Finished checking study sample table against assay tables...\n", - "2021-07-21 17:40:39,893 [INFO]: isatab.py(validate:4349) >> Loading... a_assay_2.txt\n", - "2021-07-21 17:40:39,896 [INFO]: isatab.py(validate:4357) >> Validating a_assay_2.txt against assay table configuration (transcription profiling, nucleotide sequencing)...\n", - "2021-07-21 17:40:39,897 [INFO]: isatab.py(validate:4363) >> Checking Factor Value presence...\n", - "2021-07-21 17:40:39,897 [INFO]: isatab.py(validate:4367) >> Checking required fields...\n", - "2021-07-21 17:40:39,897 [WARNING]: isatab.py(check_required_fields:3687) >> (W) Required field 'Parameter Value[library layout]' not found in the file 'a_assay_2.txt'\n", - "2021-07-21 17:40:39,898 [INFO]: isatab.py(validate:4370) >> Checking generic fields...\n", - "2021-07-21 17:40:39,900 [INFO]: isatab.py(validate:4381) >> Checking unit fields...\n", - "2021-07-21 17:40:39,901 [INFO]: isatab.py(validate:4391) >> Checking protocol fields...\n", - "2021-07-21 17:40:39,902 [WARNING]: isatab.py(check_protocol_fields:4018) >> (W) Protocol(s) of type ['library construction'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Assay Name' but has not been found, in the file 'a_assay_2.txt'\n", - "2021-07-21 17:40:39,903 [WARNING]: isatab.py(validate:4396) >> (W) There are some protocol inconsistencies in a_assay_2.txt against ('transcription profiling', 'nucleotide sequencing') configuration\n", - "2021-07-21 17:40:39,903 [INFO]: isatab.py(validate:4403) >> Checking ontology fields...\n", - "2021-07-21 17:40:39,904 [INFO]: isatab.py(validate:4416) >> Checking study group size...\n", - "2021-07-21 17:40:39,904 [INFO]: isatab.py(validate:4420) >> Finished validation on a_assay_2.txt\n", - "2021-07-21 17:40:39,905 [INFO]: isatab.py(validate:4426) >> Checking consistencies between study sample table and assay tables...\n", - "2021-07-21 17:40:39,905 [INFO]: isatab.py(validate:4431) >> Finished checking study sample table against assay tables...\n", - "2021-07-21 17:40:40,141 [INFO]: utils.py(detect_isatab_process_pooling:76) >> Checking s_study.txt\n", - "2021-07-21 17:40:40,142 [INFO]: utils.py(detect_isatab_process_pooling:85) >> Checking a_assay.txt\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:40:40,142 [INFO]: utils.py(detect_isatab_process_pooling:85) >> Checking a_assay_1.txt\n", - "2021-07-21 17:40:40,143 [INFO]: utils.py(detect_isatab_process_pooling:85) >> Checking a_assay_2.txt\n", - "2021-07-21 17:40:40,143 [INFO]: utils.py(detect_graph_process_pooling:57) >> Possible process pooling detected on: analysis\n", - "2021-07-21 17:40:40,144 [INFO]: utils.py(detect_graph_process_pooling:57) >> Possible process pooling detected on: analysis\n", - "2021-07-21 17:40:40,145 [INFO]: utils.py(detect_graph_process_pooling:57) >> Possible process pooling detected on: analysis\n", - "2021-07-21 17:40:40,145 [INFO]: isatab.py(validate:4444) >> Finished validation...\n" - ] - } - ], - "source": [ - "my_json_report = isatab.validate(open(os.path.join('./notebook-output/isa-protocol-type-assay/', 'i_investigation.txt')))" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'errors': [], 'warnings': [{'message': 'DOI is not valid format', 'supplemental': 'Found 10.1038/sdata.2016.18 in DOI field', 'code': 3002}, {'message': 'A required property is missing', 'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 1 is required', 'code': 4003}, {'message': 'A required column in assay table is not present', 'supplemental': \"Required field 'Assay Name' not found in the file 'a_assay.txt'\", 'code': 4010}, {'message': 'Missing Protocol declaration', 'supplemental': \"Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_assay.txt'\", 'code': 1007}, {'message': 'Missing Protocol declaration', 'supplemental': \"Protocol(s) of type ['library construction', 'nucleic acid sequencing'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Raw Data File' but has not been found, in the file 'a_assay.txt'\", 'code': 1007}, {'message': 'Missing Protocol declaration', 'supplemental': \"Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_assay_1.txt'\", 'code': 1007}, {'message': 'Missing Protocol declaration', 'supplemental': \"Protocol(s) of type ['library construction'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Assay Name' but has not been found, in the file 'a_assay_1.txt'\", 'code': 1007}, {'message': 'A required column in assay table is not present', 'supplemental': \"Required field 'Parameter Value[library layout]' not found in the file 'a_assay_2.txt'\", 'code': 4010}, {'message': 'Missing Protocol declaration', 'supplemental': \"Protocol(s) of type ['library construction'] defined in the ISA-configuration expected as a between 'Extract Name' and 'Assay Name' but has not been found, in the file 'a_assay_2.txt'\", 'code': 1007}], 'info': [{'message': 'Found -1 study groups in s_study.txt', 'supplemental': 'Found -1 study groups in s_study.txt', 'code': 5001}, {'message': 'Found -1 study groups in a_assay.txt', 'supplemental': 'Found -1 study groups in a_assay.txt', 'code': 5001}, {'message': 'Found -1 study groups in a_assay_1.txt', 'supplemental': 'Found -1 study groups in a_assay_1.txt', 'code': 5001}, {'message': 'Found -1 study groups in a_assay_2.txt', 'supplemental': 'Found -1 study groups in a_assay_2.txt', 'code': 5001}], 'validation_finished': True}\n" - ] - } - ], - "source": [ - "print(my_json_report)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## About this notebook\n", - "\n", - "- authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk\n", - "- license: CC-BY 4.0\n", - "- support: isatools@googlegroups.com\n", - "- issue tracker: https://github.com/ISA-tools/isa-api/issues" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.0" - } - }, - "nbformat": 4, - "nbformat_minor": 4 + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# ISA-API built-in semantic requirements for `protocol type` values\n", + "\n", + "## Abstract:\n", + "\n", + "In this notebook, we document the consequences of not using the right `protocol type` value in the context of specific ISA assays.\n", + "\n", + "It is therefore important that developers and users of the ISA-API be aware of the defautl ISA configuration and the list of protocol types used in the assay workflow associated with a given ISA Assay type, which is defined by a combination of `Measurement Type` and `Technology Type`.\n", + "\n", + "We have documented the full list of protocol types in the following document [link to document](https://www.todo.org)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Let's get the tools" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# If executing the notebooks on `Google Colab`,uncomment the following command \n", + "# and run it to install the required python libraries. Also, make the test datasets available.\n", + "\n", + "# !pip install -r requirements.txt" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import isatools\n", + "from isatools import isatab\n", + "\n", + "from isatools.model import (\n", + " Investigation,\n", + " Study,\n", + " OntologySource,\n", + " OntologyAnnotation,\n", + " Person,\n", + " Publication,\n", + " Source,\n", + " Sample,\n", + " Characteristic,\n", + " Protocol,\n", + " Process,\n", + " Assay,\n", + " Material,\n", + " DataFile,\n", + " batch_create_materials,\n", + " plink\n", + ")\n", + "import json\n", + "from isatools.isajson import ISAJSONEncoder\n", + "from isatools.isatab import dump_tables_to_dataframes" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Create an empty Investigation object and set some values to the instance variables." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "investigation = Investigation()\n", + "# investigation.identifier = \"i1\"\n", + "# investigation.title = \"My Simple ISA Investigation\"\n", + "# investigation.description = \"We could alternatively use the class constructor's parameters to set some default \" \\\n", + "# \"values at the time of creation, however we want to demonstrate how to use the \" \\\n", + "# \"object's instance variables to set values.\"\n", + "# investigation.submission_date = \"2016-11-03\"\n", + "# investigation.public_release_date = \"201611-03\"\n", + "\n", + "# Create an empty Study object and set some values. The Study must have a filename, otherwise when we serialize it\n", + "# to ISA-Tab we would not know where to write it. We must also attach the study to the investigation by adding it\n", + "# to the 'investigation' object's list of studies.\n", + "\n", + "study = Study(filename=\"s_study.txt\")\n", + "study.identifier = \"s1\"\n", + "study.title = \"My ISA Study\"\n", + "study.description = \"Like with the Investigation, we could use the class constructor to set some default values, \" \\\n", + " \"but have chosen to demonstrate in this example the use of instance variables to set initial \" \\\n", + " \"values.\"\n", + "study.submission_date = \"2016-11-03\"\n", + "study.public_release_date = \"2016-11-03\"\n", + "investigation.studies.append(study)\n", + "\n", + "# Some instance variables are typed with different objects and lists of objects. For example, a Study can have a\n", + "# list of design descriptors. A design descriptor is an Ontology Annotation describing the kind of study at hand.\n", + "# Ontology Annotations should typically reference an Ontology Source. We demonstrate a mix of using the class\n", + "# constructors and setting values with instance variables. Note that the OntologyAnnotation object\n", + "# 'intervention_design' links its 'term_source' directly to the 'obi' object instance. To ensure the OntologySource\n", + "# is encapsulated in the descriptor, it is added to a list of 'ontology_source_references' in the Investigation\n", + "# object. The 'intervention_design' object is then added to the list of 'design_descriptors' held by the Study\n", + "# object.\n", + "\n", + "obi = OntologySource(name='OBI', description=\"Ontology for Biomedical Investigations\")\n", + "investigation.ontology_source_references.append(obi)\n", + "intervention_design = OntologyAnnotation(term_source=obi)\n", + "intervention_design.term = \"intervention design\"\n", + "intervention_design.term_accession = \"http://purl.obolibrary.org/obo/OBI_0000115\"\n", + "study.design_descriptors.append(intervention_design)\n", + "\n", + "# Other instance variables common to both Investigation and Study objects include 'contacts' and 'publications',\n", + "# each with lists of corresponding Person and Publication objects.\n", + "\n", + "contact = Person(first_name=\"Alice\", last_name=\"Robertson\", affiliation=\"University of Life\", roles=[OntologyAnnotation(term='submitter')])\n", + "study.contacts.append(contact)\n", + "publication = Publication(title=\"Experiments with Elephants\", author_list=\"A. Robertson, B. Robertson\")\n", + "publication.pubmed_id = \"12345678\"\n", + "publication.doi = \"10.1038/sdata.2016.18\" #https://doi.org/10.144534/rmh0000008\"\n", + "publication.status = OntologyAnnotation(term=\"published\")\n", + "study.publications.append(publication)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Create the ISA Study graph" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# To create the study graph that corresponds to the contents of the study table file (the s_*.txt file), we need\n", + "# to create a process sequence. To do this we use the Process class and attach it to the Study object's\n", + "# 'process_sequence' list instance variable. Each process must be linked with a Protocol object that is attached to\n", + "# a Study object's 'protocols' list instance variable. The sample collection Process object usually has as input\n", + "# a Source material and as output a Sample material.\n", + "\n", + "# Here we create one Source material object and attach it to our study.\n", + "\n", + "source = Source(name='source_material')\n", + "study.sources.append(source)\n", + "\n", + "# Then we create three Sample objects, with organism as Homo Sapiens, and attach them to the study. We use the utility function\n", + "# batch_create_material() to clone a prototype material object. The function automatiaclly appends\n", + "# an index to the material name. In this case, three samples will be created, with the names\n", + "# 'sample_material-0', 'sample_material-1' and 'sample_material-2'.\n", + "\n", + "prototype_sample = Sample(name='sample_material', derives_from=(source,))\n", + "ncbitaxon = OntologySource(name='NCBITaxon', description=\"NCBI Taxonomy\")\n", + "characteristic_organism = Characteristic(category=OntologyAnnotation(term=\"Organism\"),\n", + " value=OntologyAnnotation(term=\"Homo Sapiens\", term_source=ncbitaxon,\n", + " term_accession=\"http://purl.bioontology.org/ontology/NCBITAXON/9606\"))\n", + "prototype_sample.characteristics.append(characteristic_organism)\n", + "\n", + "study.samples = batch_create_materials(prototype_sample, n=3) # creates a batch of 3 samples" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we create a single Protocol object that represents our sample collection protocol, and attach it to the\n", + "study object. Protocols must be declared before we describe Processes, as a processing event of some sort\n", + "must execute some defined protocol. In the case of the class model, Protocols should therefore be declared\n", + "before Processes in order for the Process to be linked to one." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "sample_collection_protocol = Protocol(name=\"sample collection\",\n", + " protocol_type=OntologyAnnotation(term=\"sample collection\"))\n", + "study.protocols.append(sample_collection_protocol)\n", + "sample_collection_process = Process(executes_protocol=sample_collection_protocol)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Next, we link our materials to the Process. In this particular case, we are describing a sample collection\n", + "process that takes one source material, and produces three different samples.\n", + "\n", + "(source_material)->(sample collection)->[(sample_material-0), (sample_material-1), (sample_material-2)]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "for src in study.sources:\n", + " sample_collection_process.inputs.append(src)\n", + "for sam in study.samples:\n", + " sample_collection_process.outputs.append(sam)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Finally, attach the finished Process object to the study process_sequence. This can be done many times to describe multiple sample collection events." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "study.process_sequence.append(sample_collection_process)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Building an Assay object and attach two protocols, extraction and sequencing." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Next, we build n Assay object and attach two protocols, extraction and sequencing.\n", + "\n", + "assay = Assay(filename=\"a_assay.txt\")\n", + "\n", + "extraction_protocol = Protocol(name='extraction', protocol_type=OntologyAnnotation(term=\"material extraction\"))\n", + "study.protocols.append(extraction_protocol)\n", + "\n", + "sequencing_protocol = Protocol(name='sequencing', protocol_type=OntologyAnnotation(term=\"material sequencing\"))\n", + "study.protocols.append(sequencing_protocol)\n", + "\n", + "# To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", + "# extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", + "# an extract material. The sequencing process takes the extract material and produces a data file. This will\n", + "# produce three graphs, from sample material through to data, as follows:\n", + "#\n", + "# (sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)\n", + "# (sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)\n", + "# (sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)\n", + "#\n", + "# Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", + "# graphs are NOT interconnected.\n", + "\n", + "for i, sample in enumerate(study.samples):\n", + "\n", + " # create an extraction process that executes the extraction protocol\n", + "\n", + " extraction_process = Process(executes_protocol=extraction_protocol)\n", + "\n", + " # extraction process takes as input a sample, and produces an extract material as output\n", + "\n", + " extraction_process.inputs.append(sample)\n", + " material = Material(name=\"extract-{}\".format(i))\n", + " material.type = \"Extract Name\"\n", + " extraction_process.outputs.append(material)\n", + "\n", + " # create a sequencing process that executes the sequencing protocol\n", + "\n", + " sequencing_process = Process(executes_protocol=sequencing_protocol)\n", + " sequencing_process.name = \"assay-name-{}\".format(i)\n", + " sequencing_process.inputs.append(extraction_process.outputs[0])\n", + "\n", + " # Sequencing process usually has an output data file\n", + "\n", + " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", + " sequencing_process.outputs.append(datafile)\n", + "\n", + " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", + " # these links for you. It is found in the isatools.model package\n", + "\n", + " plink(extraction_process, sequencing_process)\n", + "\n", + " # make sure the extract, data file, and the processes are attached to the assay\n", + "\n", + " assay.data_files.append(datafile)\n", + " assay.samples.append(sample)\n", + " assay.other_material.append(material)\n", + " assay.process_sequence.append(extraction_process)\n", + " assay.process_sequence.append(sequencing_process)\n", + " assay.measurement_type = OntologyAnnotation(term=\"genome sequencing\")\n", + " assay.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We start by creation an ISA Assay Object and declaring the two protocols required by the workflow." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "assay_1 = Assay(filename=\"a_assay_1.txt\")\n", + "\n", + "extraction_protocol = Protocol(name='extraction', protocol_type=OntologyAnnotation(term=\"material extraction\"))\n", + "study.protocols.append(extraction_protocol)\n", + "\n", + "sequencing_protocol_1 = Protocol(name='sequencing_1', protocol_type=OntologyAnnotation(term=\"nucleic acid sequencing\"))\n", + "study.protocols.append(sequencing_protocol_1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", + "extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", + "an extract material. The sequencing process takes the extract material and produces a data file. This will\n", + "produce three graphs, from sample material through to data, as follows:\n", + "\n", + "`(sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)`\n", + "\n", + "`(sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)`\n", + "\n", + "`(sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)`\n", + "\n", + ":warning: \n", + "Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", + "graphs are NOT interconnected." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "for i, sample in enumerate(study.samples):\n", + "\n", + " # create an extraction process that executes the extraction protocol\n", + "\n", + " extraction_process = Process(executes_protocol=extraction_protocol)\n", + "\n", + " # extraction process takes as input a sample, and produces an extract material as output\n", + "\n", + " extraction_process.inputs.append(sample)\n", + " material = Material(name=\"extract-{}\".format(i))\n", + " material.type = \"Extract Name\"\n", + " extraction_process.outputs.append(material)\n", + "\n", + " # create a sequencing process that executes the sequencing protocol\n", + "\n", + " sequencing_process = Process(executes_protocol=sequencing_protocol_1)\n", + " sequencing_process.name = \"assay-name-{}\".format(i)\n", + " sequencing_process.inputs.append(extraction_process.outputs[0])\n", + "\n", + " # Sequencing process usually has an output data file\n", + "\n", + " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", + " sequencing_process.outputs.append(datafile)\n", + "\n", + " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", + " # these links for you. It is found in the isatools.model package\n", + "\n", + " plink(extraction_process, sequencing_process)\n", + "\n", + " # make sure the extract, data file, and the processes are attached to the assay\n", + "\n", + " assay_1.data_files.append(datafile)\n", + " assay_1.samples.append(sample)\n", + " assay_1.other_material.append(material)\n", + " assay_1.process_sequence.append(extraction_process)\n", + " assay_1.process_sequence.append(sequencing_process)\n", + " assay_1.measurement_type = OntologyAnnotation(term=\"genome sequencing\")\n", + " assay_1.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Next, we build n Assay objects and attach the protocols, extraction, sequencing and a data transformation step\n", + "\n", + "assay_2 = Assay(filename=\"a_assay_2.txt\")\n", + "extraction_protocol = Protocol(name='nucleic acid extraction', protocol_type=OntologyAnnotation(term=\"nucleic acid extraction\"))\n", + "study.protocols.append(extraction_protocol)\n", + "sequencing_protocol = Protocol(name='sequencing_2', protocol_type=OntologyAnnotation(term=\"nucleic acid sequencing\"))\n", + "study.protocols.append(sequencing_protocol)\n", + "dt_protocol = Protocol(name='analysis', protocol_type=OntologyAnnotation(term=\"sequence analysis data transformation\"))\n", + "study.protocols.append(dt_protocol)\n", + "\n", + "# To build out assay graphs, we enumereate the samples from the study-level, and for each sample we create an\n", + "# extraction process and a sequencing process. The extraction process takes as input a sample material, and produces\n", + "# an extract material. The sequencing process takes the extract material and produces a data file. This will\n", + "# produce three graphs, from sample material through to data, as follows:\n", + "#\n", + "# (sample_material-0)->(extraction)->(extract-0)->(sequencing)->(sequenced-data-0)\n", + "# (sample_material-1)->(extraction)->(extract-1)->(sequencing)->(sequenced-data-1)\n", + "# (sample_material-2)->(extraction)->(extract-2)->(sequencing)->(sequenced-data-2)\n", + "#\n", + "# Note that the extraction processes and sequencing processes are distinctly separate instances, where the three\n", + "# graphs are NOT interconnected.\n", + "\n", + "for i, sample in enumerate(study.samples):\n", + "\n", + " # create an extraction process that executes the extraction protocol\n", + "\n", + " extraction_process = Process(executes_protocol=extraction_protocol)\n", + "\n", + " # extraction process takes as input a sample, and produces an extract material as output\n", + "\n", + " extraction_process.inputs.append(sample)\n", + " material = Material(name=\"extract-{}\".format(i))\n", + " material.type = \"Extract Name\"\n", + " extraction_process.outputs.append(material)\n", + "\n", + " # create a sequencing process that executes the sequencing protocol\n", + "\n", + " sequencing_process = Process(executes_protocol=sequencing_protocol)\n", + " sequencing_process.name = \"assay-name-{}\".format(i)\n", + " sequencing_process.inputs.append(extraction_process.outputs[0])\n", + "\n", + " # Sequencing process usually has an output data file\n", + "\n", + " datafile = DataFile(filename=\"sequenced-data-{}\".format(i), label=\"Raw Data File\")\n", + " sequencing_process.outputs.append(datafile)\n", + " \n", + " # Data Analysis process\n", + " dt_process = Process(executes_protocol=dt_protocol)\n", + " dt_process.name = \"dt-name-{}\".format(i)\n", + " dt_process.inputs.append(sequencing_process.outputs[0])\n", + " \n", + " derived_file = DataFile(filename=\"derived-data-{}\".format(i), label=\"Derived Data File\")\n", + " dt_process.outputs.append(derived_file)\n", + " \n", + " # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", + " # these links for you. It is found in the isatools.model package\n", + "\n", + " plink(extraction_process, sequencing_process)\n", + " plink(sequencing_process, dt_process)\n", + "\n", + " # make sure the extract, data file, and the processes are attached to the assay\n", + "\n", + " assay_2.data_files.append(datafile)\n", + " assay_2.samples.append(sample)\n", + " assay_2.other_material.append(material)\n", + " assay_2.process_sequence.append(extraction_process)\n", + " assay_2.process_sequence.append(sequencing_process)\n", + " assay_2.process_sequence.append(dt_process)\n", + " assay_2.measurement_type = OntologyAnnotation(term=\"transcription profiling\")\n", + " assay_2.technology_type = OntologyAnnotation(term=\"nucleotide sequencing\")\n", + "\n", + "\n", + "print(assay_2)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# attach the assays to the study\n", + "\n", + "study.assays.append(assay)\n", + "study.assays.append(assay_1)\n", + "study.assays.append(assay_2)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "dataframes = dump_tables_to_dataframes(investigation)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "for key in dataframes.keys():\n", + " display(key)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Inspecting the different assay tables reveals the importance of using the right strings " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "dataframes['a_assay.txt']" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "dataframes['a_assay_1.txt']" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "dataframes['a_assay_2.txt']" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "isatab.dump(investigation,'./notebook-output/isa-protocol-type-assay/') " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "my_json_report = isatab.validate(open(os.path.join('./notebook-output/isa-protocol-type-assay/', 'i_investigation.txt')))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "print(my_json_report)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## About this notebook\n", + "\n", + "- authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk\n", + "- license: CC-BY 4.0\n", + "- support: isatools@googlegroups.com\n", + "- issue tracker: https://github.com/ISA-tools/isa-api/issues" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/isa-study-design-as-json/datascriptor/crossover-study-design-4-arms-blood-derma-nmr-ms-chipseq.json b/isa-cookbook/content/notebooks/isa-study-design-as-json/datascriptor/crossover-study-design-4-arms-blood-derma-nmr-ms-chipseq.json index 47cdbcfd5..7c3de3a4d 100644 --- a/isa-cookbook/content/notebooks/isa-study-design-as-json/datascriptor/crossover-study-design-4-arms-blood-derma-nmr-ms-chipseq.json +++ b/isa-cookbook/content/notebooks/isa-study-design-as-json/datascriptor/crossover-study-design-4-arms-blood-derma-nmr-ms-chipseq.json @@ -1,1615 +1,1620 @@ -{ + { + "_id": "60d9afdcfde24e00099ec571", "name": "Chained protocols study", - "subjectType": "Homo sapiens", - "subjectSize": 10, - "designType": { - "term": "crossover design", - "id": "OBI:0500003", - "iri": "http://purl.obolibrary.org/obo/OBI_0500003", - "label": "Study subjects receive repeated treatments", - "value": "crossover" - }, - "observationalFactors": [ - { - "name": "sex", - "values": [ - "M", - "F" - ], - "isQuantitative": false, - "unit": null + "description": "A 6-month prospective, randomised, double-blinded, placebo-controlled, crossover, multicentre dietary trial is designed comparing a 9% metabolic energy based calculated medium-chain triglyceride (MCT) oil supplement to a conventional 'control' DS. Only dogs which will have an International Veterinary Epilepsy Task Force Tier II level like diagnosis of IE which satisfied the following inclusion criteria are included: age between 6 months and ≤ 12 years; weighing between 4 and ≤ 65 kg; unremarkable interictal neurological examinations; no clinically significant findings on routine laboratory diagnostics; unremarkable brain MRI scan; have had at least 3 seizures in the previous 3 months prior to enrolment; treated with at least one ASD and being classified as resistant. All dogs are fed initially for 90 ± 2 days with either the control oil or the MCT oil alongside their normal diet, followed by 97 ± 2 days with the other supplement including a 7-day washout period. Overall, the aim is to recruit thirty-six patients at five different centres and to investigate the effect of MCTs as DS on seizure activity, tolerability, behavioural comorbidities and quality of life (QoL).", + "design": + { + "subjectType": "Homo sapiens", + "subjectSize": 10, + "designType": { + "term": "crossover design", + "id": "OBI:0500003", + "iri": "http://purl.obolibrary.org/obo/OBI_0500003", + "label": "Study subjects receive repeated treatments", + "value": "crossover" }, - { - "name": "condition", - "values": [ - "healthy", - "diseased" - ], - "isQuantitative": false, - "unit": null - } - ], - "subjectGroups": { - "selected": [ - { - "name": "SubjectGroup_0", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "diseased", - "unit": null, - "isQuantitative": false - } - ] - }, + "observationalFactors": [ { - "name": "SubjectGroup_1", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "healthy", - "unit": null, - "isQuantitative": false - } - ] - }, - { - "name": "SubjectGroup_2", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "F", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "diseased", - "unit": null, - "isQuantitative": false - } - ] + "name": "sex", + "values": [ + "M", + "F" + ], + "isQuantitative": false, + "unit": null }, { - "name": "SubjectGroup_3", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "F", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "healthy", - "unit": null, - "isQuantitative": false - } - ] + "name": "condition", + "values": [ + "healthy", + "diseased" + ], + "isQuantitative": false, + "unit": null } ], - "unselected": [ - { - "name": "SubjectGroup_1", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "healthy", - "unit": null, - "isQuantitative": false - } - ] + "subjectGroups": { + "selected": [ + { + "name": "SubjectGroup_0", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "diseased", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_1", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "healthy", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_2", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "F", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "diseased", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_3", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "F", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "healthy", + "unit": null, + "isQuantitative": false + } + ] + } + ], + "unselected": [ + { + "name": "SubjectGroup_1", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "healthy", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_0", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "diseased", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_0", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "diseased", + "unit": null, + "isQuantitative": false + } + ] + }, + { + "name": "SubjectGroup_0", + "type": "Homo sapiens", + "characteristics": [ + { + "name": "sex", + "value": "M", + "unit": null, + "isQuantitative": false + }, + { + "name": "condition", + "value": "diseased", + "unit": null, + "isQuantitative": false + } + ] + } + ] + }, + "treatmentPlan": { + "screen": { + "selected": true, + "name": "screen", + "duration": 7, + "durationUnit": "days" }, - { - "name": "SubjectGroup_0", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "diseased", - "unit": null, - "isQuantitative": false - } - ] + "runIn": { + "selected": true, + "name": "run-in", + "duration": 2, + "durationUnit": "days" }, - { - "name": "SubjectGroup_0", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false - }, - { - "name": "condition", - "value": "diseased", - "unit": null, - "isQuantitative": false - } - ] + "washout": { + "selected": true, + "name": "washout", + "duration": 5, + "durationUnit": "days" }, - { - "name": "SubjectGroup_0", - "type": "Homo sapiens", - "characteristics": [ - { - "name": "sex", - "value": "M", - "unit": null, - "isQuantitative": false + "followUp": { + "selected": true, + "name": "follow-up", + "duration": 90, + "durationUnit": "days" + }, + "treatments": [ + { + "interventionType": { + "id": "ero:class:http://purl.obolibrary.org/obo/ERO_0000600", + "iri": "http://purl.obolibrary.org/obo/ERO_0000600", + "short_form": "ERO_0000600", + "obo_id": "ERO:0000600", + "label": "drug intervention", + "ontology_name": "ero", + "ontology_prefix": "ERO", + "type": "class" + }, + "agent": "ibuprofen", + "intensity": 8, + "intensityUnit": "mg/day", + "duration": 12, + "durationUnit": "days" + }, + { + "interventionType": { + "id": "ero:class:http://purl.obolibrary.org/obo/ERO_0001553", + "iri": "http://purl.obolibrary.org/obo/ERO_0001553", + "short_form": "ERO_0001553", + "obo_id": "ERO:0001553", + "label": "biologic intervention", + "ontology_name": "ero", + "ontology_prefix": "ERO", + "type": "class" }, - 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], - "Arm_2": [ - [], - [ - "blood" + }, + "selectedSampleTypes": { + "Arm_0": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] ], - [ - "blood" + "Arm_2": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] ], - [], - [ - "blood" + "Arm_5": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] ], - [ - "derma" + "Arm_7": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] ] - ], - "Arm_5": [ - [], + } + }, + { + "id": 16, + "name": "Chip-Seq", + "icon": "fa fa-dna", + "color": "red", + "measurement_type": "protein-DNA binding site identification", + "technology_type": "nucleic acid sequencing", + "workflow": [ + [ + "extraction", + { + "#replicates": { + "value": 1 + }, + "cross linking": { + "options": [ + "uv-light", + "formaldehyde", + "di-tert-butyl peroxide", + "formaldehyde and di-tert-butyl peroxyde" + ], + "values": [ + "uv-light", + "formaldehyde" + ] + }, + "DNA fragmentation": { + "options": [ + "sonication", + "nebulization", + "micrococcal nuclease digestion", + "deoxyribonuclease digestion" + ], + "values": [ + "nebulization" + ] + }, + "DNA fragment size": { + "newValues": true, + "isQuantitative": true, + "options": [ + "bbd", + "100 nm" + ], + "values": [ + "100 nm" + ] + }, + "immunoprecipitation antibody": { + "newValues": true, + "isQuantitative": true, + "options": [ + "monoclonal" + ], + "values": [ + "monoclonal" + ] + } + } + ], [ - "blood" + "extract", + { + "node_type": "extract", + "characteristics_category": "extract type", + "characteristics_value": { + "options": [ + "GENOMIC", + "GENOMIC SINGLE CELL", + "OTHER" + ], + "values": [ + "GENOMIC" + ] + }, + "is_input_to_next_protocols": { + "value": true + } + } ], [ - "blood" + "library preparation", + { + "#replicates": { + "value": 2 + }, + "library orientation": { + "options": [ + "single-end", + "paired-end" + ], + "values": [ + "single-end" + ] + }, + "library selection": { + "options": [ + "PCR", + "RANDOM-PCR", + "ChIP", + "MSLL", + "Restriction Digest", + "other", + "unspecified" + ], + "values": [ + "PCR", + "ChIP" + ] + }, + "library strategy": { + "options": [ + "Chip-Seq", + "Hi-C", + "ATAC-seq", + "ChIA-PET", + "Tethered Chromatin Conformation Capture", + "FAIRE-seq", + "OTHER" + ], + "values": [ + "Chip-Seq" + ] + } + } ], - [], [ - "blood" + "nucleic acid sequencing", + { + "#replicates": { + "value": 1 + }, + "sequencing instrument": { + "options": [ + "454 GS", + "454 GS 20", + "454 GS FLX", + "454 GS FLX+", + "454 GS FLX Titanium", + "454 GS Junior", + "HiSeq X Five", + "HiSeq X Ten", + "Illumina Genome Analyzer", + "Illumina Genome Analyzer II", + "Illumina Genome Analyzer IIx", + "Illumina HiScanSQ", + "Illumina HiSeq 1000", + "Illumina HiSeq 1500", + "Illumina HiSeq 2000", + "Illumina HiSeq 2500", + "Illumina HiSeq 3000", + "Illumina HiSeq 4000", + "Illumina iSeq 100", + "Illumina MiSeq", + "Illumina MiniSeq", + "Illumina NovaSeq 6000", + "NextSeq 500", + "NextSeq 550", + "PacBio RS", + "PacBio RS II", + "Sequel", + "Ion Torrent PGM", + "Ion Torrent Proton", + "Ion Torrent S5", + "Ion Torrent S5 XL", + "AB 3730xL Genetic Analyzer", + "AB 3730 Genetic Analyzer", + "AB 3500xL Genetic Analyzer", + "AB 3500 Genetic Analyzer", + "AB 3130xL Genetic Analyzer", + "AB 3130 Genetic Analyzer", + "AB 310 Genetic Analyzer", + "MinION", + "GridION", + "PromethION", + "BGISEQ-500", + "DNBSEQ-T7", + "DNBSEQ-G400", + "DNBSEQ-G50", + "DNBSEQ-G400 FAST", + "unspecified" + ], + "values": [ + "Illumina HiSeq 4000", + "Ion Torrent S5 XL" + ] + } + } ], [ - "derma" + "raw_data_file", + { + "node_type": "data file", + "size": 1, + "is_input_to_next_protocols": { + "value": false + } + } ] ], - "Arm_7": [ - [], - [ - "blood" + "selectedCells": { + "Arm_0": [ + false, + false, + false, + false, + false, + true ], - [ - "blood" + "Arm_2": [ + false, + false, + false, + false, + false, + true ], - [], - [ - "blood" + "Arm_5": [ + false, + false, + false, + false, + false, + true ], - [ - "derma" + "Arm_7": [ + false, + false, + false, + false, + false, + true + ] + }, + "selectedSampleTypes": { + "Arm_0": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] + ], + "Arm_2": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] + ], + "Arm_5": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] + ], + "Arm_7": [ + [], + [ + "blood" + ], + [ + "blood" + ], + [], + [ + "blood" + ], + [ + "derma" + ] ] - ] + } } - } - ] + ] + } } \ No newline at end of file diff --git a/isa-cookbook/content/notebooks/isa-tab-unused-sources-not-serialized-brapi.ipynb b/isa-cookbook/content/notebooks/isa-tab-unused-sources-not-serialized-brapi.ipynb index 9113c5438..f1f7f366d 100644 --- a/isa-cookbook/content/notebooks/isa-tab-unused-sources-not-serialized-brapi.ipynb +++ b/isa-cookbook/content/notebooks/isa-tab-unused-sources-not-serialized-brapi.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -34,7 +34,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -72,7 +72,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -84,7 +84,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -97,17 +97,9 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "T\n" - ] - } - ], + "outputs": [], "source": [ "prs = Person(last_name=\"Rocca-Serra\", first_name=\"Philippe\", mid_initials=\"T\", affiliation=\"OeRC\", email=\"prs@hotmail.com\" )\n", "prs_test_study.contacts.append(prs)\n", @@ -116,7 +108,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -135,7 +127,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -153,7 +145,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -174,7 +166,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -205,7 +197,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -222,7 +214,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -245,7 +237,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -265,7 +257,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -286,7 +278,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -303,7 +295,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -329,7 +321,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -347,7 +339,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -364,7 +356,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -380,7 +372,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -396,7 +388,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -412,7 +404,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -429,7 +421,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -445,7 +437,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -462,7 +454,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -473,7 +465,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -489,7 +481,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -498,7 +490,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -507,129 +499,25 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:44:03,166 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0, 1, 2]\n", - "2021-07-21 17:44:03,166 [WARNING]: isatab.py(write_study_table_files:1194) >> [7, 3, 0, 8, 4, 1, 9, 5, 10, 6, 2, 11]\n", - "2021-07-21 17:44:03,167 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[1, 8, 4], [1, 9, 5], [2, 10, 6]]\n", - "2021-07-21 17:44:03,187 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [6, 3]\n", - "2021-07-21 17:44:03,189 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[3, 11]]\n", - "2021-07-21 17:44:03,189 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[3, 11]]\n" - ] - } - ], + "outputs": [], "source": [ "dataframes = isatab.dump_tables_to_dataframes(investigation)" ] }, { "cell_type": "code", - "execution_count": 29, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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Source NameCharacteristics[Organism]Term Source REFTerm Accession NumberProtocol REFDatePerformerSample Name
0human individual-1Homo SapiensNCBITaxonhttp://purl.bioontology.org/ontology/NCBITAXON...sample collection2021-07-21PhilippeSBJ1_sample1
1human individual-1Homo SapiensNCBITaxonhttp://purl.bioontology.org/ontology/NCBITAXON...sample collection2021-07-21PhilippeSBJ1_sample2
2human individual-2Homo SapiensNCBITaxonhttp://purl.bioontology.org/ontology/NCBITAXON...sample collection2021-07-21PhilippeSBJ2
\n", - "
" - ], - "text/plain": [ - " Source Name Characteristics[Organism] Term Source REF \\\n", - "0 human individual-1 Homo Sapiens NCBITaxon \n", - "1 human individual-1 Homo Sapiens NCBITaxon \n", - "2 human individual-2 Homo Sapiens NCBITaxon \n", - "\n", - " Term Accession Number Protocol REF \\\n", - "0 http://purl.bioontology.org/ontology/NCBITAXON... sample collection \n", - "1 http://purl.bioontology.org/ontology/NCBITAXON... sample collection \n", - "2 http://purl.bioontology.org/ontology/NCBITAXON... sample collection \n", - "\n", - " Date Performer Sample Name \n", - "0 2021-07-21 Philippe SBJ1_sample1 \n", - "1 2021-07-21 Philippe SBJ1_sample2 \n", - "2 2021-07-21 Philippe SBJ2 " - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "dataframes['s_prs_test.txt']" ] }, { "cell_type": "code", - "execution_count": 30, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -638,22 +526,9 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:44:03,322 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [0, 1, 2]\n", - "2021-07-21 17:44:03,323 [WARNING]: isatab.py(write_study_table_files:1194) >> [7, 3, 0, 8, 4, 1, 9, 5, 10, 6, 2, 11]\n", - "2021-07-21 17:44:03,323 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[1, 8, 4], [1, 9, 5], [2, 10, 6]]\n", - "2021-07-21 17:44:03,340 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [6, 3]\n", - "2021-07-21 17:44:03,341 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[3, 11]]\n", - "2021-07-21 17:44:03,342 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[3, 11]]\n" - ] - } - ], + "outputs": [], "source": [ "%%capture\n", "isatab.dump(isa_obj=investigation, output_path=final_dir)" @@ -661,20 +536,9 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "14821" - ] - }, - "execution_count": 32, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "isa_j = json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': '))\n", "open(os.path.join(\"./notebook-output/issue-brapi\",\"isa_as_json_from_dumps.json\"),\"w\").write(isa_j) # this call write the string 'isa_j' to the file called 'isa_as_json_from_dumps.json'" @@ -682,89 +546,18 @@ }, { "cell_type": "code", - "execution_count": 33, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:44:03,364 [INFO]: isatab.py(validate:4206) >> Loading... /Users/philippe/Documents/git/isa-api2/isa-api/isa-cookbook/content/notebooks/notebook-output/issue-brapi/i_investigation.txt\n", - "2021-07-21 17:44:03,484 [INFO]: isatab.py(validate:4208) >> Running prechecks...\n", - "2021-07-21 17:44:03,494 [ERROR]: isatab.py(check_samples_not_declared_in_study_used_in_assay:2403) >> (E) Some samples in an assay file a_assay-test.txt are not declared in the study file s_prs_test.txt: ['SBJ0_sample1']\n", - "2021-07-21 17:44:03,521 [INFO]: isatab.py(validate:4229) >> Finished prechecks...\n", - "2021-07-21 17:44:03,522 [INFO]: isatab.py(validate:4230) >> Loading configurations found in /Users/philippe/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/resources/config/xml\n", - "2021-07-21 17:44:03,552 [INFO]: isatab.py(validate:4235) >> Using configurations found in /Users/philippe/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/resources/config/xml\n", - "2021-07-21 17:44:03,553 [ERROR]: isatab.py(check_measurement_technology_types:3278) >> (E) Could not load configuration for measurement type 'phenotyping' and technology type '' for STUDY ASSAY.0'\n", - "2021-07-21 17:44:03,554 [INFO]: isatab.py(validate:4237) >> Checking investigation file against configuration...\n", - "2021-07-21 17:44:03,556 [INFO]: isatab.py(validate:4240) >> Finished checking investigation file\n", - "2021-07-21 17:44:03,557 [INFO]: isatab.py(validate:4259) >> Loading... s_prs_test.txt\n", - "2021-07-21 17:44:03,560 [INFO]: isatab.py(validate:4265) >> Validating s_prs_test.txt against default study table configuration\n", - "2021-07-21 17:44:03,560 [INFO]: isatab.py(validate:4267) >> Checking Factor Value presence...\n", - "2021-07-21 17:44:03,561 [INFO]: isatab.py(validate:4270) >> Checking required fields...\n", - "2021-07-21 17:44:03,561 [INFO]: isatab.py(validate:4273) >> Checking generic fields...\n", - "2021-07-21 17:44:03,562 [INFO]: isatab.py(validate:4281) >> Checking unit fields...\n", - "2021-07-21 17:44:03,563 [INFO]: isatab.py(validate:4288) >> Checking protocol fields...\n", - "2021-07-21 17:44:03,564 [INFO]: isatab.py(validate:4298) >> Checking ontology fields...\n", - "2021-07-21 17:44:03,564 [INFO]: isatab.py(validate:4308) >> Checking study group size...\n", - "2021-07-21 17:44:03,564 [INFO]: isatab.py(validate:4312) >> Finished validation on s_prs_test.txt\n", - "2021-07-21 17:44:03,565 [ERROR]: isatab.py(validate:4336) >> Could not load config matching (phenotyping, )\n", - "2021-07-21 17:44:03,565 [WARNING]: isatab.py(validate:4340) >> Only have configs matching:\n", - "2021-07-21 17:44:03,566 [WARNING]: isatab.py(validate:4342) >> ('protein-dna binding site identification', 'dna microarray')\n", - "2021-07-21 17:44:03,566 [WARNING]: isatab.py(validate:4342) >> ('loss of heterozygosity profiling', 'dna microarray')\n", - "2021-07-21 17:44:03,567 [WARNING]: isatab.py(validate:4342) >> ('histone modification profiling', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,567 [WARNING]: isatab.py(validate:4342) >> ('dna methylation profiling', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,567 [WARNING]: isatab.py(validate:4342) >> ('protein identification', 'mass spectrometry')\n", - "2021-07-21 17:44:03,568 [WARNING]: isatab.py(validate:4342) >> ('protein-protein interaction detection', 'protein microarray')\n", - "2021-07-21 17:44:03,568 [WARNING]: isatab.py(validate:4342) >> ('snp analysis', 'dna microarray')\n", - "2021-07-21 17:44:03,569 [WARNING]: isatab.py(validate:4342) >> ('[sample]', '')\n", - "2021-07-21 17:44:03,569 [WARNING]: isatab.py(validate:4342) >> ('protein-dna binding site identification', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,570 [WARNING]: isatab.py(validate:4342) >> ('metabolite profiling', 'mass spectrometry')\n", - "2021-07-21 17:44:03,570 [WARNING]: isatab.py(validate:4342) >> ('metabolite profiling', 'nmr spectroscopy')\n", - "2021-07-21 17:44:03,571 [WARNING]: isatab.py(validate:4342) >> ('protein expression profiling', 'protein microarray')\n", - "2021-07-21 17:44:03,571 [WARNING]: isatab.py(validate:4342) >> ('cell sorting', 'flow cytometry')\n", - "2021-07-21 17:44:03,572 [WARNING]: isatab.py(validate:4342) >> ('[investigation]', '')\n", - "2021-07-21 17:44:03,573 [WARNING]: isatab.py(validate:4342) >> ('genome sequencing', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,574 [WARNING]: isatab.py(validate:4342) >> ('metagenome sequencing', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,574 [WARNING]: isatab.py(validate:4342) >> ('clinical chemistry analysis', '')\n", - "2021-07-21 17:44:03,575 [WARNING]: isatab.py(validate:4342) >> ('transcription factor binding site identification', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,575 [WARNING]: isatab.py(validate:4342) >> ('copy number variation profiling', 'dna microarray')\n", - "2021-07-21 17:44:03,576 [WARNING]: isatab.py(validate:4342) >> ('cell counting', 'flow cytometry')\n", - "2021-07-21 17:44:03,576 [WARNING]: isatab.py(validate:4342) >> ('transcription factor binding site identification', 'dna microarray')\n", - "2021-07-21 17:44:03,576 [WARNING]: isatab.py(validate:4342) >> ('protein expression profiling', 'mass spectrometry')\n", - "2021-07-21 17:44:03,577 [WARNING]: isatab.py(validate:4342) >> ('environmental gene survey', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,577 [WARNING]: isatab.py(validate:4342) >> ('transcription profiling', 'real time pcr')\n", - "2021-07-21 17:44:03,578 [WARNING]: isatab.py(validate:4342) >> ('histology', '')\n", - "2021-07-21 17:44:03,578 [WARNING]: isatab.py(validate:4342) >> ('dna methylation profiling', 'dna microarray')\n", - "2021-07-21 17:44:03,579 [WARNING]: isatab.py(validate:4342) >> ('transcription profiling', 'nucleotide sequencing')\n", - "2021-07-21 17:44:03,579 [WARNING]: isatab.py(validate:4342) >> ('protein expression profiling', 'gel electrophoresis')\n", - "2021-07-21 17:44:03,580 [WARNING]: isatab.py(validate:4342) >> ('transcription profiling', 'dna microarray')\n", - "2021-07-21 17:44:03,580 [WARNING]: isatab.py(validate:4342) >> ('hematology', '')\n", - "2021-07-21 17:44:03,581 [WARNING]: isatab.py(validate:4345) >> Skipping configuration validation as could not load config...\n", - "2021-07-21 17:44:03,581 [INFO]: isatab.py(validate:4426) >> Checking consistencies between study sample table and assay tables...\n", - "2021-07-21 17:44:03,581 [INFO]: isatab.py(validate:4431) >> Finished checking study sample table against assay tables...\n", - "2021-07-21 17:44:03,582 [INFO]: isatab.py(validate:4435) >> Skipping pooling test as there are outstanding errors\n", - "2021-07-21 17:44:03,582 [INFO]: isatab.py(validate:4444) >> Finished validation...\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "my_json_report = isatab.validate(open(os.path.join(final_dir, 'i_investigation.txt')))" ] }, { "cell_type": "code", - "execution_count": 34, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'errors': [{'message': 'Measurement/technology type invalid', 'supplemental': 'Measurement phenotyping/technology , STUDY ASSAY.0', 'code': 4002}], 'warnings': [], 'info': [{'message': 'Found -1 study groups in s_prs_test.txt', 'supplemental': 'Found -1 study groups in s_prs_test.txt', 'code': 5001}], 'validation_finished': True}\n" - ] - } - ], + "outputs": [], "source": [ "print(my_json_report)" ] @@ -784,9 +577,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -798,7 +591,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/isa_template/a_assay_genotype.txt b/isa-cookbook/content/notebooks/isa_template/a_assay_genotype.txt new file mode 100644 index 000000000..0bd2102b9 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/a_assay_genotype.txt @@ -0,0 +1,11 @@ +Sample Name Protocol REF Extract Name Protocol REF +buccal_mucosa_XOP1 DNA extraction buccal_DNA_XOG1 genotype profiling +buccal_mucosa_XOP10 DNA extraction buccal_DNA_XOG10 genotype profiling +buccal_mucosa_XOP2 DNA extraction buccal_DNA_XOG2 genotype profiling +buccal_mucosa_XOP3 DNA extraction buccal_DNA_XOG3 genotype profiling +buccal_mucosa_XOP4 DNA extraction buccal_DNA_XOG4 genotype profiling +buccal_mucosa_XOP5 DNA extraction buccal_DNA_XOG5 genotype profiling +buccal_mucosa_XOP6 DNA extraction buccal_DNA_XOG6 genotype profiling +buccal_mucosa_XOP7 DNA extraction buccal_DNA_XOG7 genotype profiling +buccal_mucosa_XOP8 DNA extraction buccal_DNA_XOG8 genotype profiling +buccal_mucosa_XOP9 DNA extraction buccal_DNA_XOG9 genotype profiling diff --git a/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_OA.txt b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_OA.txt new file mode 100644 index 000000000..d443fb6d5 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_OA.txt @@ -0,0 +1,11 @@ +Sample Name Protocol REF Parameter Value[Post Extraction] Parameter Value[Derivatization] Extract Name Protocol REF Labeled Extract Name Protocol REF Parameter Value[Chromatography Instrument] Parameter Value[Column model] Parameter Value[Column type] Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Parameter Value[Ion source] Parameter Value[Mass Analyzer] MS Assay Name Raw Spectral Data File Protocol REF Data Transformation Name Normalization Name Derived Spectral Data File Protocol REF Derived Spectral Data File Metabolite Assignment File +urine_XOP1 Extraction 1 uL pyridine oximation followed by silylation extract_XOM1 Labelling metabolites labeled_XOM1 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM1 link/to/raw/data Data transformation data_transformation_XOM1 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP10 Extraction 1 uL pyridine oximation followed by silylation extract_XOM10 Labelling metabolites labeled_XOM10 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM10 link/to/raw/data Data transformation data_transformation_XOM10 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP2 Extraction 1 uL pyridine oximation followed by silylation extract_XOM2 Labelling metabolites labeled_XOM2 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM2 link/to/raw/data Data transformation data_transformation_XOM2 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP3 Extraction 1 uL pyridine oximation followed by silylation extract_XOM3 Labelling metabolites labeled_XOM3 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM3 link/to/raw/data Data transformation data_transformation_XOM3 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP4 Extraction 1 uL pyridine oximation followed by silylation extract_XOM4 Labelling metabolites labeled_XOM4 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM4 link/to/raw/data Data transformation data_transformation_XOM4 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP5 Extraction 1 uL pyridine oximation followed by silylation extract_XOM5 Labelling metabolites labeled_XOM5 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM5 link/to/raw/data Data transformation data_transformation_XOM5 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP6 Extraction 1 uL pyridine oximation followed by silylation extract_XOM6 Labelling metabolites labeled_XOM6 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM6 link/to/raw/data Data transformation data_transformation_XOM6 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP7 Extraction 1 uL pyridine oximation followed by silylation extract_XOM7 Labelling metabolites labeled_XOM7 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM7 link/to/raw/data Data transformation data_transformation_XOM7 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP8 Extraction 1 uL pyridine oximation followed by silylation extract_XOM8 Labelling metabolites labeled_XOM8 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM8 link/to/raw/data Data transformation data_transformation_XOM8 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP9 Extraction 1 uL pyridine oximation followed by silylation extract_XOM9 Labelling metabolites labeled_XOM9 Chromatography Agilent Technologies 7890A HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um low polarity Mass spectrometry positive 50-500 Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL) EI (70 eV) single-quadrupole mass_spectrometry_XOM9 link/to/raw/data Data transformation data_transformation_XOM9 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF diff --git a/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_amines.txt b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_amines.txt new file mode 100644 index 000000000..aa24fa83d --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_amines.txt @@ -0,0 +1,11 @@ +Sample Name Protocol REF Parameter Value[Post Extraction] Parameter Value[Derivatization] Extract Name Protocol REF Labeled Extract Name Protocol REF Parameter Value[Chromatography Instrument] Parameter Value[Column model] Parameter Value[Column type] Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Parameter Value[Ion source] Parameter Value[Mass Analyzer] MS Assay Name Raw Spectral Data File Protocol REF Data Transformation Name Normalization Name Derived Spectral Data File Protocol REF Derived Spectral Data File Metabolite Assignment File +urine_XOP1 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM1 Labelling metabolites labeled_XOM1 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM1 link/to/raw/data Data transformation data_transformation_XOM1 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP10 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM10 Labelling metabolites labeled_XOM10 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM10 link/to/raw/data Data transformation data_transformation_XOM10 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP2 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM2 Labelling metabolites labeled_XOM2 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM2 link/to/raw/data Data transformation data_transformation_XOM2 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP3 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM3 Labelling metabolites labeled_XOM3 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM3 link/to/raw/data Data transformation data_transformation_XOM3 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP4 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM4 Labelling metabolites labeled_XOM4 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM4 link/to/raw/data Data transformation data_transformation_XOM4 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP5 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM5 Labelling metabolites labeled_XOM5 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM5 link/to/raw/data Data transformation data_transformation_XOM5 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP6 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM6 Labelling metabolites labeled_XOM6 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM6 link/to/raw/data Data transformation data_transformation_XOM6 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP7 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM7 Labelling metabolites labeled_XOM7 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM7 link/to/raw/data Data transformation data_transformation_XOM7 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP8 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM8 Labelling metabolites labeled_XOM8 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM8 link/to/raw/data Data transformation data_transformation_XOM8 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP9 Extraction 1 uL borate buffer (pH 8.8) with AQC reagent AQC extract_XOM9 Labelling metabolites labeled_XOM9 Chromatography Agilent 1290 Infinity II Accq-Tag Ultra column (waters + FURHTER SPECS?) reverse phase Mass spectrometry positive 5-2000? AB SCIEX Qtrap 6500 ESI triple quadrupole linear ion trap mass_spectrometry_XOM9 link/to/raw/data Data transformation data_transformation_XOM9 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF diff --git a/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_steroids.txt b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_steroids.txt new file mode 100644 index 000000000..671bde051 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/a_assay_metabolomics_steroids.txt @@ -0,0 +1,11 @@ +Sample Name Protocol REF Parameter Value[Post Extraction] Parameter Value[Derivatization] Extract Name Protocol REF Labeled Extract Name Protocol REF Parameter Value[Chromatography Instrument] Parameter Value[Column model] Parameter Value[Column type] Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Parameter Value[Ion source] Parameter Value[Mass Analyzer] MS Assay Name Raw Spectral Data File Protocol REF Data Transformation Name Normalization Name Derived Spectral Data File Protocol REF Derived Spectral Data File Metabolite Assignment File +urine_XOP1 Extraction 1 uL filtered urine NA extract_XOM1 Labelling metabolites labeled_XOM1 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM1 link/to/raw/data Data transformation data_transformation_XOM1 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP10 Extraction 1 uL filtered urine NA extract_XOM10 Labelling metabolites labeled_XOM10 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM10 link/to/raw/data Data transformation data_transformation_XOM10 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP2 Extraction 1 uL filtered urine NA extract_XOM2 Labelling metabolites labeled_XOM2 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM2 link/to/raw/data Data transformation data_transformation_XOM2 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP3 Extraction 1 uL filtered urine NA extract_XOM3 Labelling metabolites labeled_XOM3 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM3 link/to/raw/data Data transformation data_transformation_XOM3 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP4 Extraction 1 uL filtered urine NA extract_XOM4 Labelling metabolites labeled_XOM4 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM4 link/to/raw/data Data transformation data_transformation_XOM4 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP5 Extraction 1 uL filtered urine NA extract_XOM5 Labelling metabolites labeled_XOM5 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM5 link/to/raw/data Data transformation data_transformation_XOM5 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP6 Extraction 1 uL filtered urine NA extract_XOM6 Labelling metabolites labeled_XOM6 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM6 link/to/raw/data Data transformation data_transformation_XOM6 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP7 Extraction 1 uL filtered urine NA extract_XOM7 Labelling metabolites labeled_XOM7 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM7 link/to/raw/data Data transformation data_transformation_XOM7 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP8 Extraction 1 uL filtered urine NA extract_XOM8 Labelling metabolites labeled_XOM8 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM8 link/to/raw/data Data transformation data_transformation_XOM8 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF +urine_XOP9 Extraction 1 uL filtered urine NA extract_XOM9 Labelling metabolites labeled_XOM9 Chromatography Agilent 1290 Acquity UPLC CSH C18 column (Waters) reverse phase Mass spectrometry switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY? 5-3000? Agilent 6460 ESI triple quadrupole mass_spectrometry_XOM9 link/to/raw/data Data transformation data_transformation_XOM9 link/to/normalized_data link/to/spectral_file Metabolite identification link/to/data_transformation_name link/to/MAF diff --git a/isa-cookbook/content/notebooks/isa_template/a_assay_methylation.txt b/isa-cookbook/content/notebooks/isa_template/a_assay_methylation.txt new file mode 100644 index 000000000..a57833817 --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/a_assay_methylation.txt @@ -0,0 +1,11 @@ +Sample Name Protocol REF Extract Name Protocol REF +buccal_mucosa_XOP1 DNA extraction buccal_DNA_XOE1 methylation profiling +buccal_mucosa_XOP10 DNA extraction buccal_DNA_XOE10 methylation profiling +buccal_mucosa_XOP2 DNA extraction buccal_DNA_XOE2 methylation profiling +buccal_mucosa_XOP3 DNA extraction buccal_DNA_XOE3 methylation profiling +buccal_mucosa_XOP4 DNA extraction buccal_DNA_XOE4 methylation profiling +buccal_mucosa_XOP5 DNA extraction buccal_DNA_XOE5 methylation profiling +buccal_mucosa_XOP6 DNA extraction buccal_DNA_XOE6 methylation profiling +buccal_mucosa_XOP7 DNA extraction buccal_DNA_XOE7 methylation profiling +buccal_mucosa_XOP8 DNA extraction buccal_DNA_XOE8 methylation profiling +buccal_mucosa_XOP9 DNA extraction buccal_DNA_XOE9 methylation profiling diff --git a/isa-cookbook/content/notebooks/isa_template/i_investigation.txt b/isa-cookbook/content/notebooks/isa_template/i_investigation.txt new file mode 100644 index 000000000..c8f4e721a --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/i_investigation.txt @@ -0,0 +1,101 @@ +ONTOLOGY SOURCE REFERENCE +Term Source Name AFO CHEBI CHMO EDAM EFO eagle-i resource ontology MAXO MSIO NCBITAXON NCIT OBI PATO UBERON +Term Source File +Term Source Version +Term Source Description Allotrope Merged Ontology Suite Chemical Entities of Biological Interest Chemical Methods Ontology Bioinformatics operations, data types, formats, identifiers and topics Experimental Factor Ontology An ontology of research resources such as instruments, protocols, reagents, animal models and biospecimens Medical Action Ontology Metabolite Standards Initiative Ontology NCBI organismal classification NCI Thesaurus OBO Edition Ontology for Biomedical Investigations PATO - the Phenotype And Trait Ontology Uber-anatomy ontology +INVESTIGATION +Investigation Identifier tbd +Investigation Title X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data +Investigation Description Predict childhood aggression with multi-omics data and demonstrate the FAIRification process and data analysis of a multi-omics project +Investigation Submission Date +Investigation Public Release Date +INVESTIGATION PUBLICATIONS +Investigation PubMed ID +Investigation Publication DOI +Investigation Publication Author List +Investigation Publication Title +Investigation Publication Status +Investigation Publication Status Term Accession Number +Investigation Publication Status Term Source REF +INVESTIGATION CONTACTS +Investigation Person Last Name +Investigation Person First Name +Investigation Person Mid Initials +Investigation Person Email +Investigation Person Phone +Investigation Person Fax +Investigation Person Address +Investigation Person Affiliation +Investigation Person Roles +Investigation Person Roles Term Accession Number +Investigation Person Roles Term Source REF +STUDY +Study Identifier tbd +Study Title X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data +Study Description +Study Submission Date +Study Public Release Date +Study File Name s_study.txt +STUDY DESIGN DESCRIPTORS +Study Design Type +Study Design Type Term Accession Number +Study Design Type Term Source REF +STUDY PUBLICATIONS +Study PubMed ID +Study Publication DOI +Study Publication Author List +Study Publication Title +Study Publication Status +Study Publication Status Term Accession Number +Study Publication Status Term Source REF +STUDY FACTORS +Study Factor Name +Study Factor Type +Study Factor Type Term Accession Number +Study Factor Type Term Source REF +STUDY ASSAYS +Study Assay File Name a_assay_genotype.txt a_assay_methylation.txt a_assay_metabolomics_amines.txt a_assay_metabolomics_OA.txt a_assay_metabolomics_steroids.txt +Study Assay Measurement Type Methylation Beta Value targeted metabolite profiling targeted metabolite profiling targeted metabolite profiling +Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/NCIT_C164051 http://purl.obolibrary.org/obo/MSIO_0000100 http://purl.obolibrary.org/obo/MSIO_0000100 http://purl.obolibrary.org/obo/MSIO_0000100 +Study Assay Measurement Type Term Source REF NCIT MSIO MSIO MSIO +Study Assay Technology Type nucleotide sequencing DNA methylation profiling by array assay liquid chromatography-mass spectrometry gas chromatography-mass spectrometry high-performance liquid chromatography-mass spectrometry +Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0001332 http://purl.obolibrary.org/obo/CHMO_0000524 http://purl.obolibrary.org/obo/CHMO_0000796 +Study Assay Technology Type Term Source REF OBI CHMO CHMO CHMO +Study Assay Technology Platform "OntologyAnnotation( + term= + term_source=None + term_accession= + comments=0 Comment objects +)" "OntologyAnnotation( + term=Illumina Infinium MethylationEPIC BeadChip + term_source=OBI + term_accession=http://purl.obolibrary.org/obo/OBI_0002131 + comments=0 Comment objects +)" +STUDY PROTOCOLS +Study Protocol Name sample collection DNA extraction genotype profiling DNA extraction methylation profiling methylation data processing protocol urine sampling +Study Protocol Type sample collection DNA extraction genotyping DNA extraction methylation profiling Protocol urine speciment collection +Study Protocol Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000257 http://www.ebi.ac.uk/efo/EFO_0000750 http://purl.obolibrary.org/obo/OBI_0000257 http://www.ebi.ac.uk/efo/EFO_0000751 http://edamontology.org/data_2531 http://snomed.info/id/57617002 +Study Protocol Type Term Source REF OBI EFO OBI EFO EDAM EDAM +Study Protocol Description Sinke, Lucy, van Iterson, Maarten, Cats, Davy, Slieker, Roderick, & Heijmans, Bas. (2019, July 11). DNAmArray: Streamlined workflow for the quality control, normalization, and analysis of Illumina methylation array data (Version 2.1). Zenodo. http://doi.org/10.5281/zenodo.3355292 +Study Protocol URI http://doi.org/10.5281/zenodo.3355292 +Study Protocol Version +Study Protocol Parameters Name anatomical entity +Study Protocol Parameters Name Term Accession Number http://purl.obolibrary.org/obo/UBERON_0001062 +Study Protocol Parameters Name Term Source REF UBERON +Study Protocol Components Name +Study Protocol Components Type +Study Protocol Components Type Term Accession Number +Study Protocol Components Type Term Source REF +STUDY CONTACTS +Study Person Last Name +Study Person First Name +Study Person Mid Initials +Study Person Email +Study Person Phone +Study Person Fax +Study Person Address +Study Person Affiliation +Study Person Roles +Study Person Roles Term Accession Number +Study Person Roles Term Source REF diff --git a/isa-cookbook/content/notebooks/isa_template/s_study.txt b/isa-cookbook/content/notebooks/isa_template/s_study.txt new file mode 100644 index 000000000..a97ec89dd --- /dev/null +++ b/isa-cookbook/content/notebooks/isa_template/s_study.txt @@ -0,0 +1,21 @@ +Source Name Characteristics[organism] Term Source REF Term Accession Number Characteristics[family ID] Characteristics[childhood aggressive behaviour measurement] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[anatomical entity] Sample Name Characteristics[organism part] Term Source REF Term Accession Number Characteristics[sample type] Term Source REF Term Accession Number +XOP1 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF1 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP1 +XOP1 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF1 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP1 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP10 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF10 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP10 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP10 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF10 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP10 +XOP2 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF2 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP2 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP2 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF2 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP2 +XOP3 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF3 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP3 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP3 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF3 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP3 +XOP4 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF4 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP4 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP4 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF4 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP4 +XOP5 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF5 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP5 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP5 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF5 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP5 +XOP6 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF6 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP6 +XOP6 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF6 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP6 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP7 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF7 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP7 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP7 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF7 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP7 +XOP8 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF8 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP8 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 +XOP8 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF8 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP8 +XOP9 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF9 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection buccal mucosa buccal_mucosa_XOP9 +XOP9 Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 XOF9 0 T-score NCIT http://purl.obolibrary.org/obo/NCIT_C120401 sample collection urine urine_XOP9 urine UBERON http://purl.obolibrary.org/obo/UBERON_0001088 experimental sample CHMO http://purl.obolibrary.org/obo/CHMO_0002746 diff --git a/isa-cookbook/content/notebooks/json/BII-S-3/BII-S-3.json b/isa-cookbook/content/notebooks/json/BII-S-3/BII-S-3.json index 6f5da5ddb..3eb196683 100644 --- a/isa-cookbook/content/notebooks/json/BII-S-3/BII-S-3.json +++ b/isa-cookbook/content/notebooks/json/BII-S-3/BII-S-3.json @@ -1,5 +1,5 @@ { - "publicReleaseDate": "", + "publicReleaseDate": "2000-01-01", "comments": [ { "name": "Last Opened With Configuration", @@ -11,7 +11,7 @@ } ], "identifier": "BII-S-3", - "submissionDate": "", + "submissionDate": "2000-01-01", "description": "", "people": [], "studies": [ @@ -209,7 +209,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay4.1", "outputs": [ @@ -239,7 +239,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_21", @@ -258,7 +258,7 @@ "@id": "#protocol/genomic_DNA_extraction_-_standard_procedure_4" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -280,7 +280,7 @@ "@id": "#protocol/genomic_DNA_extraction_-_standard_procedure_4" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -299,7 +299,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay1", "outputs": [ @@ -329,7 +329,7 @@ "@id": "#protocol/genomic_DNA_extraction_-_standard_procedure_4" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -351,7 +351,7 @@ "@id": "#protocol/genomic_DNA_extraction_-_standard_procedure_4" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -373,7 +373,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_23", @@ -389,7 +389,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay4.2", "outputs": [ @@ -416,7 +416,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay3.1", "outputs": [ @@ -446,7 +446,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction2", @@ -487,7 +487,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_22", @@ -506,7 +506,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction3", @@ -544,7 +544,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay2", "outputs": [ @@ -574,7 +574,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction1", @@ -615,7 +615,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_24", @@ -631,7 +631,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay3.2", "outputs": [ @@ -661,7 +661,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction4", @@ -962,7 +962,7 @@ "@id": "#protocol/mRNA_extraction_-_standard_procedure_3" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -984,7 +984,7 @@ "@id": "#protocol/mRNA_extraction_-_standard_procedure_3" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -1006,7 +1006,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction4", @@ -1052,7 +1052,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.1", "outputs": [ @@ -1079,7 +1079,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.4", "outputs": [ @@ -1109,7 +1109,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_21", @@ -1125,7 +1125,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.1", "outputs": [ @@ -1152,7 +1152,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.1", "outputs": [ @@ -1179,7 +1179,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.2", "outputs": [ @@ -1206,7 +1206,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.5", "outputs": [ @@ -1233,7 +1233,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.3", "outputs": [ @@ -1260,7 +1260,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.5", "outputs": [ @@ -1287,7 +1287,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.1", "outputs": [ @@ -1317,7 +1317,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction3", @@ -1363,7 +1363,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.5", "outputs": [ @@ -1393,7 +1393,7 @@ "@id": "#protocol/mRNA_extraction_-_standard_procedure_3" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -1415,7 +1415,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction1", @@ -1461,7 +1461,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.6", "outputs": [ @@ -1488,7 +1488,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.5", "outputs": [ @@ -1515,7 +1515,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.3", "outputs": [ @@ -1542,7 +1542,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.3", "outputs": [ @@ -1572,7 +1572,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_22", @@ -1591,7 +1591,7 @@ "@id": "#protocol/mRNA_extraction_-_standard_procedure_3" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -1610,7 +1610,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.6", "outputs": [ @@ -1637,7 +1637,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.6", "outputs": [ @@ -1664,7 +1664,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.3", "outputs": [ @@ -1691,7 +1691,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.6", "outputs": [ @@ -1718,7 +1718,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.2", "outputs": [ @@ -1748,7 +1748,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_23", @@ -1764,7 +1764,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.2", "outputs": [ @@ -1794,7 +1794,7 @@ "@id": "#protocol/library_construction" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/library_construction2", @@ -1840,7 +1840,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay6.4", "outputs": [ @@ -1867,7 +1867,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay7.4", "outputs": [ @@ -1897,7 +1897,7 @@ "@id": "#protocol/nucleic_acid_extraction_-_standard_procedure_2" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [], "@id": "#process/nucleic_acid_extraction_-_standard_procedure_24", @@ -1913,7 +1913,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay5.2", "outputs": [ @@ -1940,7 +1940,7 @@ "@id": "#protocol/pyrosequencing_-_standard_procedure_6" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "name": "assay8.4", "outputs": [ @@ -2479,7 +2479,7 @@ "@id": "#protocol/environmental_material_collection_-_standard_procedure_1" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -2509,7 +2509,7 @@ "@id": "#protocol/environmental_material_collection_-_standard_procedure_1" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -2539,7 +2539,7 @@ "@id": "#protocol/environmental_material_collection_-_standard_procedure_1" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { @@ -2569,7 +2569,7 @@ "@id": "#protocol/environmental_material_collection_-_standard_procedure_1" }, "comments": [], - "date": "", + "date": "2000-01-01", "performer": "", "outputs": [ { diff --git a/isa-cookbook/content/notebooks/light-sensitity-study-repeated-treatment-design.ipynb b/isa-cookbook/content/notebooks/light-sensitity-study-repeated-treatment-design.ipynb index c71e2e1ab..f4ea67d46 100644 --- a/isa-cookbook/content/notebooks/light-sensitity-study-repeated-treatment-design.ipynb +++ b/isa-cookbook/content/notebooks/light-sensitity-study-repeated-treatment-design.ipynb @@ -1,1015 +1,738 @@ { - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Light Sensitivity Experiment: \n", - "\n", - "## Reporting a repeated treatment design with `ISA create mode`\n", - "\n", - "This example creates `ISA study descriptor` for study with sequential treatments organized in an arm. This shows how to use objects from the `isatools.create` component in a granular fashion. It creates each `Element` of the Study `Arm` at a time.\n", - "Finally, the `study design plan` is shown by serializing the `ISA Study Design Model` content as an `ISA_design` JSON document, which can be rendered in various ways (tables, figures)." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Study metadata" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "# If executing the notebooks on `Google Colab`,uncomment the following command \n", - "# and run it to install the required python libraries. Also, make the test datasets available.\n", - "\n", - "# !pip install -r requirements.txt" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "import os\n", - "import datetime\n", - "import json\n", - "from collections import OrderedDict\n", - "from isatools.model import (\n", - " Investigation,\n", - " Study,\n", - " Sample,\n", - " OntologyAnnotation,\n", - " StudyFactor,\n", - " FactorValue,\n", - " Characteristic,\n", - " Source,\n", - " Protocol,\n", - " Process\n", - ")\n", - "from isatools.create.model import (\n", - " Treatment,\n", - " NonTreatment,\n", - " StudyDesign,\n", - " StudyCell,\n", - " StudyArm,\n", - " ProductNode,\n", - " SampleAndAssayPlan,\n", - " AssayGraph\n", - ")\n", - "from isatools.create.constants import (\n", - " BASE_FACTORS,\n", - " SCREEN,\n", - " RUN_IN,\n", - " WASHOUT,\n", - " FOLLOW_UP,\n", - " SAMPLE,\n", - " EXTRACT,\n", - " LABELED_EXTRACT,\n", - " DATA_FILE\n", - ")\n", - "from isatools.isatab import dumps\n", - "from isatools.isajson import ISAJSONEncoder\n" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "investigation = Investigation()\n", - "investigation1 = Investigation() # to be used with the study create function\n", - "study = Study(filename=\"s_study_xover.txt\")\n", - "study.identifier = \"elifesprint2019-1\"\n", - "study.title = \"elifesprint2019-1: light sensitivity\"\n", - "study.description = \"a study about light sensitivity difference between a control population (n=10) and a genotype A population (n=10).\"\n", - "study.submission_date = str(datetime.datetime.today())\n", - "study.public_release_date = str(datetime.datetime.today())\n", - "study.sources = [Source(name=\"source1\")]\n", - "study.samples = [Sample(name=\"sample1\")]\n", - "study.protocols = [Protocol(name=\"sample collection\")]\n", - "study.process_sequence = [Process(executes_protocol=study.protocols[-1], inputs=[study.sources[-1]], outputs=[study.samples[-1]])]\n", - "investigation.studies = [study]\n" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/plain": [ - "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[], publications=[], contacts=[], studies=[isatools.model.Study(filename='s_study_xover.txt', identifier='elifesprint2019-1', title='elifesprint2019-1: light sensitivity', description='a study about light sensitivity difference between a control population (n=10) and a genotype A population (n=10).', submission_date='2021-07-21 17:43:54.131318', public_release_date='2021-07-21 17:43:54.131358', contacts=[], design_descriptors=[], publications=[], factors=[], protocols=[isatools.model.Protocol(name='sample collection', protocol_type=isatools.model.OntologyAnnotation(term='', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[])], assays=[], sources=[isatools.model.Source(name='source1', characteristics=[], comments=[])], samples=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[], comments=[])], process_sequence=[isatools.model.Process(id=\"\". name=\"None\", executes_protocol=Protocol(\n", - " name=sample collection\n", - " protocol_type=\n", - " uri=\n", - " version=\n", - " parameters=0 ProtocolParameter objects\n", - " components=0 OntologyAnnotation objects\n", - " comments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='source1', characteristics=[], comments=[])], outputs=[isatools.model.Sample(name='sample1', characteristics=[], factor_values=[], derives_from=[], comments=[])])], other_material=[], characteristic_categories=[], comments=[], units=[])], comments=[])" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Let's see the object :\n", - "investigation" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# print(dumps(investigation))" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1. Creation of the first `ISA Study Design Element` and setting *both* `element_type` AND `duration_unit` attributes" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "NonTreatment(\n", - " type='screen',\n", - " duration=isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=0.0, unit=isatools.model.OntologyAnnotation(term='days', term_source=None, term_accession='', comments=[]))\n", - " )\n" - ] - } - ], - "source": [ - "# IMPORTANT: note how duration_unit value is supplied as an OntologyAnnotation object\n", - "nte1 = NonTreatment(element_type='screen', duration_unit=OntologyAnnotation(term=\"days\"))\n", - "print(nte1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 2. Creation of another `ISA Study Design Element`, of type `Treatment`" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=radiological intervention, \n", - " factor_values=[])\n", - " \n" - ] - } - ], - "source": [ - "te1 = Treatment()\n", - "te1.type='radiological intervention'\n", - "print(te1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 2.1 defining the first treatment as a vector of ISA factor values:\n", - "\n", - "Under \"ISA Study Design Create mode\", a `Study Design Element` of type `Treatment` needs to be defined by a vector of `Factors` and their respective associated `Factor Values`. This is done as follows:" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "FactorValue(\n", - " factor_name=light\n", - " value='visible light at 3000K produced by LED array'\n", - " unit=\n", - ") FactorValue(\n", - " factor_name=dose\n", - " value=250\n", - " unit=lux\n", - ")\n" - ] - } - ], - "source": [ - "\n", - "f1 = StudyFactor(name='light', factor_type=OntologyAnnotation(term=\"electromagnetic energy\"))\n", - "f1v = FactorValue(factor_name=f1, value=\"visible light at 3000K produced by LED array\")\n", - "f2 = StudyFactor(name='dose', factor_type=OntologyAnnotation(term=\"quantity\"))\n", - "\n", - "# IMPORTANT: note how *FactorValue value* is supplied as an *numeral*\n", - "f2v = FactorValue(factor_name=f2, value=250, unit=OntologyAnnotation(term='lux'))\n", - "f3 = StudyFactor(name='duration', factor_type=OntologyAnnotation(term=\"time\"))\n", - "f3v = FactorValue(factor_name=f3, value=1, unit=OntologyAnnotation(term='hr'))\n", - "\n", - "print(f1v,f2v)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=radiological intervention, \n", - " factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='quantity', term_source=None, term_accession='', comments=[]), comments=[]), value=250, unit=isatools.model.OntologyAnnotation(term='lux', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=isatools.model.OntologyAnnotation(term='hr', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='light', factor_type=isatools.model.OntologyAnnotation(term='electromagnetic energy', term_source=None, term_accession='', comments=[]), comments=[]), value='visible light at 3000K produced by LED array', unit=None)])\n", - " \n" - ] - } - ], - "source": [ - "#assigning the factor values declared above to the ISA treatment element\n", - "te1.factor_values = [f1v,f2v,f3v]\n", - "print(te1)\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 3. Creation of a second `ISA Study Design Element`, of type `Treatment`, following the same pattern." - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"Treatment\n", - " (type=radiological intervention, \n", - " factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='quantity', term_source=None, term_accession='', comments=[]), comments=[]), value=250, unit=isatools.model.OntologyAnnotation(term='lux', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=1, unit=isatools.model.OntologyAnnotation(term='hour', term_source=None, term_accession='', comments=[])), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='light', factor_type=isatools.model.OntologyAnnotation(term='electromagnetic energy', term_source=None, term_accession='', comments=[]), comments=[]), value='visible light at 3000K produced by LED array', unit=None)])\n", - " \n" - ] - } - ], - "source": [ - "te3 = Treatment()\n", - "te3.type = 'radiological intervention'\n", - "rays = StudyFactor(name='light', factor_type=OntologyAnnotation(term=\"electromagnetic energy\"))\n", - "\n", - "raysv = FactorValue(factor_name=rays, value='visible light at 3000K produced by LED array')\n", - "rays_intensity = StudyFactor(name='dose', factor_type=OntologyAnnotation(term=\"quantity\"))\n", - "rays_intensityv= FactorValue(factor_name=rays_intensity, value = 250, unit=OntologyAnnotation(term='lux'))\n", - "rays_duration = StudyFactor(name = 'duration', factor_type=OntologyAnnotation(term=\"time\"))\n", - "rays_durationv = FactorValue(factor_name=rays_duration, value=1, unit=OntologyAnnotation(term='hour'))\n", - "\n", - "te3.factor_values = [raysv,rays_intensityv,rays_durationv]\n", - "print(te3)\n", - " " - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 4. Creation of 'wash out' period as an `ISA Study Design Element`." - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "NonTreatment(\n", - " type='washout',\n", - " duration=isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='DURATION', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=None, term_accession='', comments=[]), comments=[]), value=0.0, unit=isatools.model.OntologyAnnotation(term='days', term_source=None, term_accession='', comments=[]))\n", - " )\n" - ] - } - ], - "source": [ - "# Creation of another ISA element, which is not a Treatment element, which is of type `screen` by default\n", - "# nte2 = NonTreatment()\n", - "# nte2.type = 'washout'\n", - "# net2.duration_unit=OntologyAnnotation(term=\"days\")\n", - "\n", - "nte2 = NonTreatment(element_type='washout', duration_unit=OntologyAnnotation(term=\"days\"))\n", - "print(nte2)" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# setting the factor values associated with 'default' DURATION Factor associated with such elements\n", - "nte2.duration.value=2\n", - "nte2.duration.unit=OntologyAnnotation(term=\"weeks\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 5. Creation of 'follow-up' period as an `ISA Study Design Element`." - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "nte3 = NonTreatment(element_type='follow-up', duration_value=1, duration_unit=OntologyAnnotation(term=\"month\"))\n", - "#print(nte3)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 6. Creation of the associated container, known as an ISA `Cell` for each ISA `Element`.\n", - "In this example, a single `Element` is hosted by a `Cell`, which must be named. In more complex designs (e.g. study designs with assymetric arms), a `Cell` may contain more than one `Element`, hence the list attribute." - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "st_cl1= StudyCell(name=\"st_cl1\", elements=[nte1])\n", - "st_cl2= StudyCell(name=\"st_cl2\", elements=[te1])\n", - "st_cl3= StudyCell(name=\"st_cl3\", elements=[nte2])\n", - "st_cl4= StudyCell(name=\"st_cl4\", elements=[te3])\n", - "st_cl5= StudyCell(name=\"st_cl5\", elements=[nte3])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 7. Creation of an ISA `Study Arm` and setting the number of subjects associated to that unique sequence of ISA `Cell`s." - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": { - "scrolled": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\"StudyArm(\n", - " name=Arm 1,\n", - " source_type=Characteristic(\n", - " category=genotype\n", - " value=control - normal\n", - " unit=\n", - " comments=0 Comment objects\n", - "),\n", - " group_size=2, \n", - " no. cells=0,\n", - " no. sample_assay_plans=0\n", - " )\n" - ] - } - ], - "source": [ - "genotype_cat = OntologyAnnotation(term=\"genotype\")\n", - "genotype_value1 = OntologyAnnotation(term=\"control - normal\")\n", - "genotype_value2 = OntologyAnnotation(term=\"mutant\")\n", - "\n", - "arm1 = StudyArm(\n", - " name='Arm 1', \n", - " group_size=2\n", - ")\n", - "\n", - "arm1.source_type=Characteristic(\n", - " category=genotype_cat,\n", - " value=genotype_value1\n", - ")\n", - "\n", - "print(arm1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 8. Declaring an ISA `Sample Assay Plan`, defining which `Sample` are to be collected and which `Assay`s to be used" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "whole_patient=ProductNode(\n", - " id_=\"MAT1\",\n", - " name=\"subject\",\n", - " node_type=SAMPLE,\n", - " size=1,\n", - " characteristics=[\n", - " Characteristic(\n", - " category=OntologyAnnotation(term='organism part'), \n", - " value=OntologyAnnotation(term='whole organism')\n", - " )\n", - " ]\n", - ")\n", - "\n", - "saliva=ProductNode(\n", - " id_=\"MAT2\",\n", - " name=\"saliva\",\n", - " node_type=SAMPLE,\n", - " size=1,\n", - " characteristics=[\n", - " Characteristic(\n", - " category=OntologyAnnotation(term='organism part'),\n", - " value=OntologyAnnotation(term='saliva')\n", - " )\n", - " ]\n", - ")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Here we load an isa assay definition in the form of an ordered dictionary. It corresponds to an ISA configuration assay table but expressed in JSON." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We now show how to create an new AssayGraph structure from scratch, as if we were defining a completely new assay type." - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "light_sensitivity_phenotyping_1 = OrderedDict([\n", - " ('measurement_type', OntologyAnnotation(term='melatonine concentration')),\n", - " ('technology_type', OntologyAnnotation(term='radioimmunoprecipitation assay')),\n", - " ('extraction', {}),\n", - " ('extract', [\n", - " {\n", - " 'node_type': EXTRACT,\n", - " 'characteristics_category': OntologyAnnotation(term='extract type'),\n", - " 'characteristics_value': OntologyAnnotation(term='extract'),\n", - " 'size': 1,\n", - " 'technical_replicates': None,\n", - " 'is_input_to_next_protocols': True\n", - " }]),\n", - " \n", - " ('radioimmunoprecipitation', {\n", - " OntologyAnnotation(term='instrument'): [OntologyAnnotation(term='Beckon Dickison XYZ')],\n", - " OntologyAnnotation(term='antibody'): [OntologyAnnotation(term='AbCam antiMelatonine ')],\n", - " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", - " OntologyAnnotation(term='2 hr')]\n", - " }),\n", - " ('raw_data_file', [\n", - " {\n", - " 'node_type': DATA_FILE,\n", - " 'size': 1,\n", - " 'technical_replicates': 1,\n", - " 'is_input_to_next_protocols': False\n", - " }\n", - " ])\n", - "])\n", - "\n", - "\n", - "light_sensitivity_phenotyping_2 = OrderedDict([\n", - " ('measurement_type', OntologyAnnotation(term='light sensitivity')),\n", - " ('technology_type', OntologyAnnotation(term='electroencephalography')),\n", - " ('data_collection', {\n", - " OntologyAnnotation(term='instrument'): [OntologyAnnotation(term='Somnotouch')],\n", - " OntologyAnnotation(term='sampling_rate'): [OntologyAnnotation(term='200 Hz')],\n", - " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", - " OntologyAnnotation(term='2 hr')]\n", - " }),\n", - " ('raw_data_file', [\n", - " {\n", - " 'node_type': DATA_FILE,\n", - " 'size': 1,\n", - " 'technical_replicates': 1,\n", - " 'is_input_to_next_protocols': False\n", - " }\n", - " ])\n", - "])\n", - "\n", - "light_sensitivity_phenotyping_3 = OrderedDict([\n", - " ('measurement_type', OntologyAnnotation(term='light sensitivity phenotyping')),\n", - " ('technology_type', OntologyAnnotation(term='direct measurement')),\n", - " ('data_collection', {\n", - " OntologyAnnotation(term='variables'): [OntologyAnnotation(term='sleepiness'),\n", - " OntologyAnnotation(term='heart rate'),\n", - " OntologyAnnotation(term='pupilla size')],\n", - " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", - " OntologyAnnotation(term='2 hr')]\n", - " }),\n", - " ('raw_data_file', [\n", - " {\n", - " 'node_type': DATA_FILE,\n", - " 'size': 1,\n", - " 'technical_replicates': 1,\n", - " 'is_input_to_next_protocols': False\n", - " }\n", - " ])\n", - "])\n" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "alterness_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_1)\n", - "melatonine_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_2)\n", - "general_phenotyping_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_3)" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "\n", - "sap1 = SampleAndAssayPlan(name='sap1', sample_plan=[whole_patient,saliva],assay_plan=[alterness_assay_graph,melatonine_assay_graph,general_phenotyping_assay_graph])\n", - "\n", - "sap1.add_element_to_map(sample_node=saliva, assay_graph=melatonine_assay_graph)\n", - "sap1.add_element_to_map(sample_node=whole_patient, assay_graph=alterness_assay_graph)\n", - "sap1.add_element_to_map(sample_node=whole_patient,assay_graph=general_phenotyping_assay_graph)\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 9. Declaration of an ISA assay and linking specimen type and data acquisition plan for this assay" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/plain": [ - "{isatools.create.model.ProductNode(id=MAT2, type=sample, name=saliva, characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='saliva', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], size=1, extension=None): {isatools.create.model.AssayGraph(id=cce3713d-dfd3-4942-8d87-cb391156d756, measurement_type=OntologyAnnotation(\n", - " term=light sensitivity\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), technology_type=OntologyAnnotation(\n", - " term=electroencephalography\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), nodes={isatools.create.model.ProductNode(id=raw_data_file_000_001, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=data_collection_001, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Somnotouch', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='sampling_rate', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='200 Hz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='2 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProtocolNode(id=data_collection_000, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Somnotouch', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='sampling_rate', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='200 Hz', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_000, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None)}, links=[('data_collection_000', 'raw_data_file_000_000'), ('data_collection_001', 'raw_data_file_000_001')], quality_control=None)},\n", - " isatools.create.model.ProductNode(id=MAT1, type=sample, name=subject, characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='organism part', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='whole organism', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], size=1, extension=None): {isatools.create.model.AssayGraph(id=05599bfb-d02b-471e-b9b1-6ce6758791db, measurement_type=OntologyAnnotation(\n", - " term=melatonine concentration\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), technology_type=OntologyAnnotation(\n", - " term=radioimmunoprecipitation assay\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), nodes={isatools.create.model.ProductNode(id=extract_000_000, type=extract, name=extract, characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='extract type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='extract', term_source=None, term_accession='', comments=[]), unit=None, comments=[])], size=1, extension=None), isatools.create.model.ProtocolNode(id=extraction_000, name=assay0 - extraction, protocol_type=OntologyAnnotation(\n", - " term=assay0 - extraction\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[]), isatools.create.model.ProtocolNode(id=radioimmunoprecipitation_001_000, name=assay0 - radioimmunoprecipitation, protocol_type=OntologyAnnotation(\n", - " term=assay0 - radioimmunoprecipitation\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Beckon Dickison XYZ', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='antibody', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='AbCam antiMelatonine ', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='2 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_001, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=radioimmunoprecipitation_000_000, name=assay0 - radioimmunoprecipitation, protocol_type=OntologyAnnotation(\n", - " term=assay0 - radioimmunoprecipitation\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='instrument', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='Beckon Dickison XYZ', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='antibody', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='AbCam antiMelatonine ', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_000, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None)}, links=[('extract_000_000', 'radioimmunoprecipitation_000_000'), ('extract_000_000', 'radioimmunoprecipitation_001_000'), ('extraction_000', 'extract_000_000'), ('radioimmunoprecipitation_000_000', 'raw_data_file_000_000'), ('radioimmunoprecipitation_001_000', 'raw_data_file_000_001')], quality_control=None),\n", - " isatools.create.model.AssayGraph(id=d7726069-1823-4f49-b10c-8856036ad082, measurement_type=OntologyAnnotation(\n", - " term=light sensitivity phenotyping\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), technology_type=OntologyAnnotation(\n", - " term=direct measurement\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), nodes={isatools.create.model.ProductNode(id=raw_data_file_000_002, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProductNode(id=raw_data_file_000_003, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=data_collection_004, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='pupilla size', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_004, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=data_collection_000, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='sleepiness', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_001, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=data_collection_002, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='heart rate', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='1 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProtocolNode(id=data_collection_005, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='pupilla size', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='2 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProtocolNode(id=data_collection_003, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='heart rate', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='2 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_005, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None), isatools.create.model.ProtocolNode(id=data_collection_001, name=assay0 - data_collection, protocol_type=OntologyAnnotation(\n", - " term=assay0 - data_collection\n", - " term_source=\n", - " term_accession=\n", - " comments=0 Comment objects\n", - " ), uri=, description=, version=, parameter_values=[isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='variables', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='sleepiness', term_source=None, term_accession='', comments=[]), unit=None, comments=[]), isatools.model.ParameterValue(category=isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='time point', term_source=None, term_accession='', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='2 hr', term_source=None, term_accession='', comments=[]), unit=None, comments=[])]), isatools.create.model.ProductNode(id=raw_data_file_000_000, type=data file, name=raw_data_file, characteristics=[], size=1, extension=None)}, links=[('data_collection_000', 'raw_data_file_000_000'), ('data_collection_001', 'raw_data_file_000_001'), ('data_collection_002', 'raw_data_file_000_002'), ('data_collection_003', 'raw_data_file_000_003'), ('data_collection_004', 'raw_data_file_000_004'), ('data_collection_005', 'raw_data_file_000_005')], quality_control=None)}}" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sap1.sample_to_assay_map" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 10. Build an ISA `Study Design Arm` by adding the first set of ISA `Cells` and setting the `Sample Assay Plan`" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "arm1.add_item_to_arm_map(st_cl1, sap1)\n", - "# print(arm1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 11 Now expanding the `Arm` by adding a new `Cell`, which uses the same `Sample Assay Plan` as the one used in Cell #1.\n", - "Of course, the `Sample Assay Plan` for this new `Cell` could be different. It would have to be to built as shown before." - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "arm1.add_item_to_arm_map(st_cl2, sap1)" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# Adding the last section of the Arm, with a cell which also uses the same sample assay plan.\n", - "arm1.add_item_to_arm_map(st_cl3, sap1)\n", - "arm1.add_item_to_arm_map(st_cl4, sap1)\n", - "arm1.add_item_to_arm_map(st_cl5, sap1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 12. Creation of additional ISA Study Arms and setting the number of subjects associated to that unique sequence of ISA Cells." - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "arm2 = StudyArm(name='Arm 2')\n", - "arm2.group_size=2\n", - "arm2.source_type=Characteristic(category=genotype_cat,\n", - " value=genotype_value2)\n", - "\n", - "# st_cl6= StudyCell(name=\"st_cl6\", elements=[nte1])\n", - "# st_cl7= StudyCell(name=\"st_cl7\", elements=[te1])\n", - "# st_cl8= StudyCell(name=\"st_cl8\", elements=[nte2])\n", - "# st_cl9= StudyCell(name=\"st_cl9\", elements=[te3])\n", - "# st_cl10= StudyCell(name=\"st_cl10\", elements=[nte3])\n", - "\n", - "\n", - "\n", - "arm2.source_type.category\n", - "arm2.add_item_to_arm_map(st_cl1,sap1)\n", - "arm2.add_item_to_arm_map(st_cl4,sap1)\n", - "arm2.add_item_to_arm_map(st_cl3,sap1)\n", - "arm2.add_item_to_arm_map(st_cl2,sap1)\n", - "arm2.add_item_to_arm_map(st_cl5,sap1)" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "arm3 = StudyArm(name='Arm 3')\n", - "arm3.group_size=2\n", - "arm3.source_type=Characteristic(category=genotype_cat,\n", - " value=genotype_value1\n", - " )\n", - "arm3.add_item_to_arm_map(st_cl1,sap1)\n", - "arm3.add_item_to_arm_map(st_cl2,sap1)\n", - "arm3.add_item_to_arm_map(st_cl3,sap1)\n", - "arm3.add_item_to_arm_map(st_cl4,sap1)\n", - "arm3.add_item_to_arm_map(st_cl5,sap1)" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "arm4 = StudyArm(name='Arm 4')\n", - "arm4.group_size=2\n", - "arm4.source_type=Characteristic(category=genotype_cat,\n", - " value=genotype_value2)\n", - "\n", - "arm4.add_item_to_arm_map(st_cl1,sap1)\n", - "arm4.add_item_to_arm_map(st_cl4,None)\n", - "arm4.add_item_to_arm_map(st_cl3,sap1)\n", - "arm4.add_item_to_arm_map(st_cl2,None)\n", - "arm4.add_item_to_arm_map(st_cl5,sap1)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 14. We can now create the ISA `Study Design` object, which will receive the `Arms` defined by the user." - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "study_design_final= StudyDesign(name='trial design #1')\n", - "# print(sd)" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# Adding a study arm to the study design object.\n", - "study_design_final.add_study_arm(arm1)\n", - "study_design_final.add_study_arm(arm2)\n", - "study_design_final.add_study_arm(arm3)\n", - "study_design_final.add_study_arm(arm4)\n", - "\n", - "study_finale = study_design_final.generate_isa_study()\n", - "investigation1.studies.append(study_finale)\n", - "# print(investigation1.studies[0].name)" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "# Let's now serialize the ISA study design to JSON\n", - "from isatools.create.model import StudyDesignEncoder\n", - "\n", - "f=json.dumps(study_design_final, cls=StudyDesignEncoder, sort_keys=True, indent=4, separators=(',', ': '))\n", - "\n", - "final_dir = os.path.abspath(os.path.join('notebook-output', 'isa-study-custom-assay-light-sensitivity'))\n", - "\n", - "with open(os.path.join(final_dir,'./light-sensitivity-study_design_final.json'), 'w') as isa_sdf_jf:\n", - " json.dump(json.loads(f), isa_sdf_jf)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-07-21 17:43:54,822 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [3, 4, 5, 6]\n", - "2021-07-21 17:43:54,828 [WARNING]: isatab.py(write_study_table_files:1194) >> [8, 7, 3, 10, 9, 12, 11, 14, 13, 16, 15, 18, 17, 20, 19, 22, 21, 24, 23, 26, 25, 28, 27, 30, 29, 32, 31, 34, 33, 36, 35, 38, 37, 40, 39, 42, 41, 44, 43, 46, 45, 48, 47, 4, 50, 49, 52, 51, 54, 53, 56, 55, 58, 57, 60, 59, 62, 61, 64, 63, 66, 65, 68, 67, 70, 69, 72, 71, 74, 73, 76, 75, 78, 77, 80, 79, 82, 81, 84, 83, 86, 85, 88, 87, 5, 90, 89, 92, 91, 94, 93, 96, 95, 98, 97, 100, 99, 102, 101, 104, 103, 106, 105, 108, 107, 110, 109, 112, 111, 114, 113, 116, 115, 118, 117, 120, 119, 122, 121, 124, 123, 126, 125, 128, 127, 6, 130, 129, 132, 131, 134, 133, 136, 135, 138, 137, 140, 139, 142, 141, 144, 143, 146, 145, 148, 147, 150, 149]\n", - "2021-07-21 17:43:54,829 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[3, 8, 7], [3, 10, 9], [3, 12, 11], [3, 14, 13], [3, 16, 15], [3, 18, 17], [3, 20, 19], [3, 22, 21], [3, 24, 23], [3, 26, 25], [3, 28, 27], [3, 30, 29], [3, 32, 31], [3, 34, 33], [3, 36, 35], [3, 38, 37], [3, 40, 39], [3, 42, 41], [3, 44, 43], [3, 46, 45], [4, 48, 47], [4, 50, 49], [4, 52, 51], [4, 54, 53], [4, 56, 55], [4, 58, 57], [4, 60, 59], [4, 62, 61], [4, 64, 63], [4, 66, 65], [4, 68, 67], [4, 70, 69], [4, 72, 71], [4, 74, 73], [4, 76, 75], [4, 78, 77], [4, 80, 79], [4, 82, 81], [4, 84, 83], [4, 86, 85], [5, 88, 87], [5, 90, 89], [5, 92, 91], [5, 94, 93], [5, 96, 95], [5, 98, 97], [5, 100, 99], [5, 102, 101], [5, 104, 103], [5, 106, 105], [5, 108, 107], [5, 110, 109], [5, 112, 111], [5, 114, 113], [5, 116, 115], [5, 118, 117], [5, 120, 119], [5, 122, 121], [5, 124, 123], [5, 126, 125], [6, 130, 129], [6, 132, 131], [6, 134, 133], [6, 136, 135], [6, 138, 137], [6, 140, 139], [6, 142, 141], [6, 144, 143], [6, 146, 145], [6, 148, 147], [6, 150, 149], [6, 128, 127]]\n" - ] - }, - { - "ename": "KeyError", - "evalue": "'Sample Name.0.Factor Value[DURATION]'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/ipykernel_17990/2479725034.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m# print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0misatools\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0misatab\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0misatab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdump\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfinal_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0misatools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misatab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdump_tables_to_dataframes\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mdumpdf\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/isatab.py\u001b[0m in \u001b[0;36mdump\u001b[0;34m(isa_obj, output_path, i_file_name, skip_dump_tables, write_factor_values_in_assay_table)\u001b[0m\n\u001b[1;32m 1047\u001b[0m \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1048\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1049\u001b[0;31m \u001b[0mwrite_study_table_files\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minvestigation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1050\u001b[0m write_assay_table_files(\n\u001b[1;32m 1051\u001b[0m investigation, output_path, write_factor_values_in_assay_table)\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_study_table_files\u001b[0;34m(inv_obj, output_dir)\u001b[0m\n\u001b[1;32m 1295\u001b[0m fvlabel = \"{0}.Factor Value[{1}]\".format(\n\u001b[1;32m 1296\u001b[0m olabel, fv.factor_name.name)\n\u001b[0;32m-> 1297\u001b[0;31m \u001b[0mwrite_value_columns\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfvlabel\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1298\u001b[0m \"\"\"if isinstance(pbar, ProgressBar):\n\u001b[1;32m 1299\u001b[0m pbar.finish()\"\"\"\n", - "\u001b[0;32m~/.pyenv/versions/3.9.0/envs/isa-api-py39/lib/python3.9/site-packages/isatools/isatab.py\u001b[0m in \u001b[0;36mwrite_value_columns\u001b[0;34m(df_dict, label, x)\u001b[0m\n\u001b[1;32m 1715\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1716\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mOntologyAnnotation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1717\u001b[0;31m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1718\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mterm\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1719\u001b[0m \u001b[0mdf_dict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlabel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\".Unit.Term Source REF\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mKeyError\u001b[0m: 'Sample Name.0.Factor Value[DURATION]'" - ] - } - ], - "source": [ - "# print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))\n", - "from isatools import isatab\n", - "from isatools.isatab import dump_tables_to_dataframes as dumpdf\n", - "\n", - "isatab.dump(investigation1, final_dir)\n", - "\n", - "dataframes = dumpdf(investigation)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## About this notebook\n", - "\n", - "- authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk\n", - "- license: CC-BY 4.0\n", - "- support: isatools@googlegroups.com\n", - "- issue tracker: https://github.com/ISA-tools/isa-api/issues" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "isa-api-py39", - "language": "python", - "name": "isa-api-py39" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.0" - } - }, - "nbformat": 4, - "nbformat_minor": 1 + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Light Sensitivity Experiment: \n", + "\n", + "## Reporting a repeated treatment design with `ISA create mode`\n", + "\n", + "This example creates `ISA study descriptor` for study with sequential treatments organized in an arm. This shows how to use objects from the `isatools.create` component in a granular fashion. It creates each `Element` of the Study `Arm` at a time.\n", + "Finally, the `study design plan` is shown by serializing the `ISA Study Design Model` content as an `ISA_design` JSON document, which can be rendered in various ways (tables, figures)." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Study metadata" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "# If executing the notebooks on `Google Colab`,uncomment the following command \n", + "# and run it to install the required python libraries. Also, make the test datasets available.\n", + "\n", + "# !pip install -r requirements.txt" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import datetime\n", + "import json\n", + "from collections import OrderedDict\n", + "from isatools.model import (\n", + " Investigation,\n", + " Study,\n", + " Sample,\n", + " OntologyAnnotation,\n", + " StudyFactor,\n", + " FactorValue,\n", + " Characteristic,\n", + " Source,\n", + " Protocol,\n", + " Process\n", + ")\n", + "from isatools.create.model import (\n", + " Treatment,\n", + " NonTreatment,\n", + " StudyDesign,\n", + " StudyCell,\n", + " StudyArm,\n", + " ProductNode,\n", + " SampleAndAssayPlan,\n", + " AssayGraph\n", + ")\n", + "from isatools.create.constants import (\n", + " BASE_FACTORS,\n", + " SCREEN,\n", + " RUN_IN,\n", + " WASHOUT,\n", + " FOLLOW_UP,\n", + " SAMPLE,\n", + " EXTRACT,\n", + " LABELED_EXTRACT,\n", + " DATA_FILE\n", + ")\n", + "from isatools.isatab import dumps\n", + "from isatools.isajson import ISAJSONEncoder\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "investigation = Investigation()\n", + "investigation1 = Investigation() # to be used with the study create function\n", + "study = Study(filename=\"s_study_xover.txt\")\n", + "study.identifier = \"elifesprint2019-1\"\n", + "study.title = \"elifesprint2019-1: light sensitivity\"\n", + "study.description = \"a study about light sensitivity difference between a control population (n=10) and a genotype A population (n=10).\"\n", + "study.submission_date = str(datetime.datetime.today())\n", + "study.public_release_date = str(datetime.datetime.today())\n", + "study.sources = [Source(name=\"source1\")]\n", + "study.samples = [Sample(name=\"sample1\")]\n", + "study.protocols = [Protocol(name=\"sample collection\")]\n", + "study.process_sequence = [Process(executes_protocol=study.protocols[-1], inputs=[study.sources[-1]], outputs=[study.samples[-1]])]\n", + "investigation.studies = [study]\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "# Let's see the object :\n", + "investigation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# print(dumps(investigation))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1. Creation of the first `ISA Study Design Element` and setting *both* `element_type` AND `duration_unit` attributes" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# IMPORTANT: note how duration_unit value is supplied as an OntologyAnnotation object\n", + "nte1 = NonTreatment(element_type='screen', duration_unit=OntologyAnnotation(term=\"days\"))\n", + "print(nte1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 2. Creation of another `ISA Study Design Element`, of type `Treatment`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "te1 = Treatment()\n", + "te1.type='radiological intervention'\n", + "print(te1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 2.1 defining the first treatment as a vector of ISA factor values:\n", + "\n", + "Under \"ISA Study Design Create mode\", a `Study Design Element` of type `Treatment` needs to be defined by a vector of `Factors` and their respective associated `Factor Values`. This is done as follows:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "f1 = StudyFactor(name='light', factor_type=OntologyAnnotation(term=\"electromagnetic energy\"))\n", + "f1v = FactorValue(factor_name=f1, value=\"visible light at 3000K produced by LED array\")\n", + "f2 = StudyFactor(name='dose', factor_type=OntologyAnnotation(term=\"quantity\"))\n", + "\n", + "# IMPORTANT: note how *FactorValue value* is supplied as an *numeral*\n", + "f2v = FactorValue(factor_name=f2, value=250, unit=OntologyAnnotation(term='lux'))\n", + "f3 = StudyFactor(name='duration', factor_type=OntologyAnnotation(term=\"time\"))\n", + "f3v = FactorValue(factor_name=f3, value=1, unit=OntologyAnnotation(term='hr'))\n", + "\n", + "print(f1v,f2v)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#assigning the factor values declared above to the ISA treatment element\n", + "te1.factor_values = [f1v,f2v,f3v]\n", + "print(te1)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 3. Creation of a second `ISA Study Design Element`, of type `Treatment`, following the same pattern." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "te3 = Treatment()\n", + "te3.type = 'radiological intervention'\n", + "rays = StudyFactor(name='light', factor_type=OntologyAnnotation(term=\"electromagnetic energy\"))\n", + "\n", + "raysv = FactorValue(factor_name=rays, value='visible light at 3000K produced by LED array')\n", + "rays_intensity = StudyFactor(name='dose', factor_type=OntologyAnnotation(term=\"quantity\"))\n", + "rays_intensityv= FactorValue(factor_name=rays_intensity, value = 250, unit=OntologyAnnotation(term='lux'))\n", + "rays_duration = StudyFactor(name = 'duration', factor_type=OntologyAnnotation(term=\"time\"))\n", + "rays_durationv = FactorValue(factor_name=rays_duration, value=1, unit=OntologyAnnotation(term='hour'))\n", + "\n", + "te3.factor_values = [raysv,rays_intensityv,rays_durationv]\n", + "print(te3)\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 4. Creation of 'wash out' period as an `ISA Study Design Element`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Creation of another ISA element, which is not a Treatment element, which is of type `screen` by default\n", + "# nte2 = NonTreatment()\n", + "# nte2.type = 'washout'\n", + "# net2.duration_unit=OntologyAnnotation(term=\"days\")\n", + "\n", + "nte2 = NonTreatment(element_type='washout', duration_unit=OntologyAnnotation(term=\"days\"))\n", + "print(nte2)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# setting the factor values associated with 'default' DURATION Factor associated with such elements\n", + "nte2.duration.value=2\n", + "nte2.duration.unit=OntologyAnnotation(term=\"weeks\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 5. Creation of 'follow-up' period as an `ISA Study Design Element`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "nte3 = NonTreatment(element_type='follow-up', duration_value=1, duration_unit=OntologyAnnotation(term=\"month\"))\n", + "#print(nte3)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 6. Creation of the associated container, known as an ISA `Cell` for each ISA `Element`.\n", + "In this example, a single `Element` is hosted by a `Cell`, which must be named. In more complex designs (e.g. study designs with assymetric arms), a `Cell` may contain more than one `Element`, hence the list attribute." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "st_cl1= StudyCell(name=\"st_cl1\", elements=[nte1])\n", + "st_cl2= StudyCell(name=\"st_cl2\", elements=[te1])\n", + "st_cl3= StudyCell(name=\"st_cl3\", elements=[nte2])\n", + "st_cl4= StudyCell(name=\"st_cl4\", elements=[te3])\n", + "st_cl5= StudyCell(name=\"st_cl5\", elements=[nte3])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 7. Creation of an ISA `Study Arm` and setting the number of subjects associated to that unique sequence of ISA `Cell`s." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "genotype_cat = OntologyAnnotation(term=\"genotype\")\n", + "genotype_value1 = OntologyAnnotation(term=\"control - normal\")\n", + "genotype_value2 = OntologyAnnotation(term=\"mutant\")\n", + "\n", + "arm1 = StudyArm(\n", + " name='Arm 1', \n", + " group_size=2\n", + ")\n", + "\n", + "arm1.source_type=Characteristic(\n", + " category=genotype_cat,\n", + " value=genotype_value1\n", + ")\n", + "\n", + "print(arm1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 8. Declaring an ISA `Sample Assay Plan`, defining which `Sample` are to be collected and which `Assay`s to be used" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "whole_patient=ProductNode(\n", + " id_=\"MAT1\",\n", + " name=\"subject\",\n", + " node_type=SAMPLE,\n", + " size=1,\n", + " characteristics=[\n", + " Characteristic(\n", + " category=OntologyAnnotation(term='organism part'), \n", + " value=OntologyAnnotation(term='whole organism')\n", + " )\n", + " ]\n", + ")\n", + "\n", + "saliva=ProductNode(\n", + " id_=\"MAT2\",\n", + " name=\"saliva\",\n", + " node_type=SAMPLE,\n", + " size=1,\n", + " characteristics=[\n", + " Characteristic(\n", + " category=OntologyAnnotation(term='organism part'),\n", + " value=OntologyAnnotation(term='saliva')\n", + " )\n", + " ]\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Here we load an isa assay definition in the form of an ordered dictionary. It corresponds to an ISA configuration assay table but expressed in JSON." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We now show how to create an new AssayGraph structure from scratch, as if we were defining a completely new assay type." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "light_sensitivity_phenotyping_1 = OrderedDict([\n", + " ('measurement_type', OntologyAnnotation(term='melatonine concentration')),\n", + " ('technology_type', OntologyAnnotation(term='radioimmunoprecipitation assay')),\n", + " ('extraction', {}),\n", + " ('extract', [\n", + " {\n", + " 'node_type': EXTRACT,\n", + " 'characteristics_category': OntologyAnnotation(term='extract type'),\n", + " 'characteristics_value': OntologyAnnotation(term='extract'),\n", + " 'size': 1,\n", + " 'technical_replicates': None,\n", + " 'is_input_to_next_protocols': True\n", + " }]),\n", + " \n", + " ('radioimmunoprecipitation', {\n", + " OntologyAnnotation(term='instrument'): [OntologyAnnotation(term='Beckon Dickison XYZ')],\n", + " OntologyAnnotation(term='antibody'): [OntologyAnnotation(term='AbCam antiMelatonine ')],\n", + " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", + " OntologyAnnotation(term='2 hr')]\n", + " }),\n", + " ('raw_data_file', [\n", + " {\n", + " 'node_type': DATA_FILE,\n", + " 'size': 1,\n", + " 'technical_replicates': 1,\n", + " 'is_input_to_next_protocols': False\n", + " }\n", + " ])\n", + "])\n", + "\n", + "\n", + "light_sensitivity_phenotyping_2 = OrderedDict([\n", + " ('measurement_type', OntologyAnnotation(term='light sensitivity')),\n", + " ('technology_type', OntologyAnnotation(term='electroencephalography')),\n", + " ('data_collection', {\n", + " OntologyAnnotation(term='instrument'): [OntologyAnnotation(term='Somnotouch')],\n", + " OntologyAnnotation(term='sampling_rate'): [OntologyAnnotation(term='200 Hz')],\n", + " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", + " OntologyAnnotation(term='2 hr')]\n", + " }),\n", + " ('raw_data_file', [\n", + " {\n", + " 'node_type': DATA_FILE,\n", + " 'size': 1,\n", + " 'technical_replicates': 1,\n", + " 'is_input_to_next_protocols': False\n", + " }\n", + " ])\n", + "])\n", + "\n", + "light_sensitivity_phenotyping_3 = OrderedDict([\n", + " ('measurement_type', OntologyAnnotation(term='light sensitivity phenotyping')),\n", + " ('technology_type', OntologyAnnotation(term='direct measurement')),\n", + " ('data_collection', {\n", + " OntologyAnnotation(term='variables'): [OntologyAnnotation(term='sleepiness'),\n", + " OntologyAnnotation(term='heart rate'),\n", + " OntologyAnnotation(term='pupilla size')],\n", + " OntologyAnnotation(term='time point'): [OntologyAnnotation(term='1 hr'),\n", + " OntologyAnnotation(term='2 hr')]\n", + " }),\n", + " ('raw_data_file', [\n", + " {\n", + " 'node_type': DATA_FILE,\n", + " 'size': 1,\n", + " 'technical_replicates': 1,\n", + " 'is_input_to_next_protocols': False\n", + " }\n", + " ])\n", + "])\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "alterness_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_1)\n", + "melatonine_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_2)\n", + "general_phenotyping_assay_graph = AssayGraph.generate_assay_plan_from_dict(light_sensitivity_phenotyping_3)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "\n", + "sap1 = SampleAndAssayPlan(name='sap1', sample_plan=[whole_patient,saliva],assay_plan=[alterness_assay_graph,melatonine_assay_graph,general_phenotyping_assay_graph])\n", + "\n", + "sap1.add_element_to_map(sample_node=saliva, assay_graph=melatonine_assay_graph)\n", + "sap1.add_element_to_map(sample_node=whole_patient, assay_graph=alterness_assay_graph)\n", + "sap1.add_element_to_map(sample_node=whole_patient,assay_graph=general_phenotyping_assay_graph)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 9. Declaration of an ISA assay and linking specimen type and data acquisition plan for this assay" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "sap1.sample_to_assay_map" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 10. Build an ISA `Study Design Arm` by adding the first set of ISA `Cells` and setting the `Sample Assay Plan`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "arm1.add_item_to_arm_map(st_cl1, sap1)\n", + "# print(arm1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 11 Now expanding the `Arm` by adding a new `Cell`, which uses the same `Sample Assay Plan` as the one used in Cell #1.\n", + "Of course, the `Sample Assay Plan` for this new `Cell` could be different. It would have to be to built as shown before." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "arm1.add_item_to_arm_map(st_cl2, sap1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Adding the last section of the Arm, with a cell which also uses the same sample assay plan.\n", + "arm1.add_item_to_arm_map(st_cl3, sap1)\n", + "arm1.add_item_to_arm_map(st_cl4, sap1)\n", + "arm1.add_item_to_arm_map(st_cl5, sap1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 12. Creation of additional ISA Study Arms and setting the number of subjects associated to that unique sequence of ISA Cells." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "arm2 = StudyArm(name='Arm 2')\n", + "arm2.group_size=2\n", + "arm2.source_type=Characteristic(category=genotype_cat,\n", + " value=genotype_value2)\n", + "\n", + "# st_cl6= StudyCell(name=\"st_cl6\", elements=[nte1])\n", + "# st_cl7= StudyCell(name=\"st_cl7\", elements=[te1])\n", + "# st_cl8= StudyCell(name=\"st_cl8\", elements=[nte2])\n", + "# st_cl9= StudyCell(name=\"st_cl9\", elements=[te3])\n", + "# st_cl10= StudyCell(name=\"st_cl10\", elements=[nte3])\n", + "\n", + "\n", + "\n", + "arm2.source_type.category\n", + "arm2.add_item_to_arm_map(st_cl1,sap1)\n", + "arm2.add_item_to_arm_map(st_cl4,sap1)\n", + "arm2.add_item_to_arm_map(st_cl3,sap1)\n", + "arm2.add_item_to_arm_map(st_cl2,sap1)\n", + "arm2.add_item_to_arm_map(st_cl5,sap1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "arm3 = StudyArm(name='Arm 3')\n", + "arm3.group_size=2\n", + "arm3.source_type=Characteristic(category=genotype_cat,\n", + " value=genotype_value1\n", + " )\n", + "arm3.add_item_to_arm_map(st_cl1,sap1)\n", + "arm3.add_item_to_arm_map(st_cl2,sap1)\n", + "arm3.add_item_to_arm_map(st_cl3,sap1)\n", + "arm3.add_item_to_arm_map(st_cl4,sap1)\n", + "arm3.add_item_to_arm_map(st_cl5,sap1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "arm4 = StudyArm(name='Arm 4')\n", + "arm4.group_size=2\n", + "arm4.source_type=Characteristic(category=genotype_cat,\n", + " value=genotype_value2)\n", + "\n", + "arm4.add_item_to_arm_map(st_cl1,sap1)\n", + "arm4.add_item_to_arm_map(st_cl4,None)\n", + "arm4.add_item_to_arm_map(st_cl3,sap1)\n", + "arm4.add_item_to_arm_map(st_cl2,None)\n", + "arm4.add_item_to_arm_map(st_cl5,sap1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 14. We can now create the ISA `Study Design` object, which will receive the `Arms` defined by the user." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "study_design_final= StudyDesign(name='trial design #1')\n", + "# print(sd)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Adding a study arm to the study design object.\n", + "study_design_final.add_study_arm(arm1)\n", + "study_design_final.add_study_arm(arm2)\n", + "study_design_final.add_study_arm(arm3)\n", + "study_design_final.add_study_arm(arm4)\n", + "\n", + "study_finale = study_design_final.generate_isa_study()\n", + "investigation1.studies.append(study_finale)\n", + "# print(investigation1.studies[0].name)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Let's now serialize the ISA study design to JSON\n", + "from isatools.create.model import StudyDesignEncoder\n", + "\n", + "f=json.dumps(study_design_final, cls=StudyDesignEncoder, sort_keys=True, indent=4, separators=(',', ': '))\n", + "\n", + "final_dir = os.path.abspath(os.path.join('notebook-output', 'isa-study-custom-assay-light-sensitivity'))\n", + "\n", + "with open(os.path.join(final_dir,'./light-sensitivity-study_design_final.json'), 'w') as isa_sdf_jf:\n", + " json.dump(json.loads(f), isa_sdf_jf)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "# print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))\n", + "from isatools import isatab\n", + "from isatools.isatab import dump_tables_to_dataframes as dumpdf\n", + "\n", + "isatab.dump(investigation1, final_dir)\n", + "\n", + "dataframes = dumpdf(investigation)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## About this notebook\n", + "\n", + "- authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk\n", + "- license: CC-BY 4.0\n", + "- support: isatools@googlegroups.com\n", + "- issue tracker: https://github.com/ISA-tools/isa-api/issues" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 } diff --git a/isa-cookbook/content/notebooks/output/BII-S-9/a_gilbert-assay-Gx.txt b/isa-cookbook/content/notebooks/output/BII-S-9/a_gilbert-assay-Gx.txt deleted file mode 100644 index c458be99d..000000000 --- a/isa-cookbook/content/notebooks/output/BII-S-9/a_gilbert-assay-Gx.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Extract Name Material Type Protocol REF Assay Name Raw Data File Comment[data_comment] -GSM255770.a1 nucleic acid extraction extract-0 pellet nucleic acid sequencing assay-name-0 sequenced-data-0 data_value -GSM255771.a1 nucleic acid extraction extract-1 pellet nucleic acid sequencing assay-name-1 sequenced-data-1 data_value -GSM255772.a1 nucleic acid extraction extract-2 pellet nucleic acid sequencing assay-name-2 sequenced-data-2 data_value -GSM255773.a1 nucleic acid extraction extract-3 pellet nucleic acid sequencing assay-name-3 sequenced-data-3 data_value diff --git a/isa-cookbook/content/notebooks/output/BII-S-9/i_investigation.txt b/isa-cookbook/content/notebooks/output/BII-S-9/i_investigation.txt deleted file mode 100644 index 0778018c1..000000000 --- a/isa-cookbook/content/notebooks/output/BII-S-9/i_investigation.txt +++ /dev/null @@ -1,99 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name CHEBI EFO OBI PATO NCIBTaxon -Term Source File -Term Source Version -Term Source Description Chemical Entity of Biological Interest Experimental Factor Ontology Ontology for Biomedical Investigations Phenotype and Trait Ontology NCBI Taxonomy -INVESTIGATION -Investigation Identifier -Investigation Title -Investigation Description -Investigation Submission Date -Investigation Public Release Date -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier BII-S-9-synth -Study Title cross-omics synthetic experiment -Study Description cross-omics experiment testing ISA-API support for sample aliquoting at study or assay level -Study Submission Date 15/08/2021 -Study Public Release Date 15/08/2021 -Study File Name s_BII-S-9-synthesic.txt -Comment[SRA Broker Name] OXFORD -Comment[SRA Center Name] OXFORD -Comment[SRA Center Project Name] OXFORD -Comment[SRA Lab Name] Oxford e-Research Centre -Comment[SRA Submission Action] ADD -Comment[Study Funding Agency] -Comment[Study Grant Number] -STUDY DESIGN DESCRIPTORS -Study Design Type intervention design -Study Design Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000115 -Study Design Type Term Source REF OBI -STUDY PUBLICATIONS -Study PubMed ID 18725995 -Study Publication DOI 10.1371/journal.pone.0003042 -Study Publication Author List Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. -Study Publication Title Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. -Study Publication Status indexed in PubMed -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name compound dose collection time -Study Factor Type chemical substance dose time -Study Factor Type Term Accession Number http://purl.obolibrary.org/obo/CHEBI_59999 http://www.ebi.ac.uk/efo/EFO_0000428 http://purl.obolibrary.org/obo/PATO_0000165 -Study Factor Type Term Source REF CHEBI EFO PATO -STUDY ASSAYS -Study Assay File Name a_gilbert-assay-Gx.txt -Study Assay Measurement Type metagenome sequencing -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0002623 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type nucleotide sequencing -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform -STUDY PROTOCOLS -Study Protocol Name environmental material collection - standard procedure 1 nucleic acid extraction sample aliquoting - standard procedure 3 genomic DNA extraction - standard procedure 4 reverse transcription - standard procedure 5 library construction nucleic acid sequencing sequence analysis - standard procedure 7 -Study Protocol Type sample collection nucleic acid extraction aliquoting nucleic acid extraction reverse transcription library construction nucleic acid sequencing data transformation -Study Protocol Type Term Accession Number -Study Protocol Type Term Source REF -Study Protocol Description Waters samples were prefiltered through a 1.6 um GF/A glass fibre filter to reduce Eukaryotic contamination. Filtrate was then collected on a 0.2 um Sterivex (millipore) filter which was frozen in liquid nitrogen until nucelic acid extraction. CO2 bubbled through 11000 L mesocosm to simulate ocean acidification predicted conditions. Then phosphate and nitrate were added to induce a phytoplankton bloom. Total nucleic acid extraction was done as quickly as possible using the method of Neufeld et al, 2007. splitting collected samples into aliquots superscript+random hexamer primer 1. Sample Input and Fragmentation: The Genome Sequencer FLX System supports the sequencing of samples from a wide variety of starting materials including genomic DNA, PCR products, BACs, and cDNA. Samples such as genomic DNA and BACs are fractionated into small, 300- to 800-base pair fragments. For smaller samples, such as small non-coding RNA or PCR amplicons, fragmentation is not required. Instead, short PCR products amplified using Genome Sequencer fusion primers can be used for immobilization onto DNA capture beads as shown below. -Study Protocol URI -Study Protocol Version -Study Protocol Parameters Name filter pore size library strategy;library layout;library selection sequencing instrument -Study Protocol Parameters Name Term Accession Number ;; -Study Protocol Parameters Name Term Source REF ;; -Study Protocol Components Name -Study Protocol Components Type -Study Protocol Components Type Term Accession Number -Study Protocol Components Type Term Source REF -STUDY CONTACTS -Study Person Last Name Durand -Study Person First Name Rex -Study Person Mid Initials -Study Person Email rex.durand@lhcl.ac.uk -Study Person Phone -Study Person Fax -Study Person Address Nevsky perspective, Bournemouth, United Kingdom -Study Person Affiliation LHC Laboratory -Study Person Roles principal investigator role;SRA Inform On Status;SRA Inform On Error -Study Person Roles Term Accession Number ;; -Study Person Roles Term Source REF ;; -Comment[Study Person REF] diff --git a/isa-cookbook/content/notebooks/output/BII-S-9/s_BII-S-9-synthesic.txt b/isa-cookbook/content/notebooks/output/BII-S-9/s_BII-S-9-synthesic.txt deleted file mode 100644 index 7372b0b51..000000000 --- a/isa-cookbook/content/notebooks/output/BII-S-9/s_BII-S-9-synthesic.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[Organism] Term Source REF Term Accession Number Protocol REF Sample Name Factor Value[compound] Factor Value[dose] Factor Value[collection time] Protocol REF Sample Name -GSM255770 marine metagenome NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_408172 environmental material collection - standard procedure 1 GSM255770 atorvastatin high dose 2 months sample aliquoting - standard procedure 3 GSM255770.a1 -GSM255771 marine metagenome NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_408172 environmental material collection - standard procedure 1 GSM255771 atorvastatin low dose 2 months sample aliquoting - standard procedure 3 GSM255771.a1 -GSM255772 marine metagenome NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_408172 environmental material collection - standard procedure 1 GSM255772 atorvastatin high dose 18 months sample aliquoting - standard procedure 3 GSM255772.a1 -GSM255773 marine metagenome NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_408172 environmental material collection - standard procedure 1 GSM255773 atorvastatin low dose 18 months sample aliquoting - standard procedure 3 GSM255773.a1 diff --git a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_isotopologue-ms-assay.txt b/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_isotopologue-ms-assay.txt deleted file mode 100644 index 33eaef0a7..000000000 --- a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_isotopologue-ms-assay.txt +++ /dev/null @@ -1,9 +0,0 @@ -Sample Name Factor Value[compound] Factor Value[dose] Factor Value[duration] Protocol REF Extract Name Material Type Characteristics[quantity] Unit Protocol REF Parameter Value[chromatography column] Parameter Value[mass spectrometry instrument] Parameter Value[mass analyzer] MS Assay Name Spectral Raw Data File Comment[data_comment] Protocol REF Parameter Value[ms software] Data Transformation Name Derived Data File -culture-1-sample-0 dioxygen high hour intracellular metabolite extraction extract-ms-0 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-0 ms-data-0.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-1-sample-1 dioxygen high hour intracellular metabolite extraction extract-ms-2 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-2 ms-data-2.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-1-sample-2 dioxygen high hour intracellular metabolite extraction extract-ms-4 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-4 ms-data-4.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-1-sample-3 dioxygen high hour intracellular metabolite extraction extract-ms-6 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-6 ms-data-6.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-2-sample-0 dioxygen normal hour intracellular metabolite extraction extract-ms-1 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-1 ms-data-1.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-2-sample-1 dioxygen normal hour intracellular metabolite extraction extract-ms-3 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-3 ms-data-3.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-2-sample-2 dioxygen normal hour intracellular metabolite extraction extract-ms-5 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-5 ms-data-5.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt -culture-2-sample-3 dioxygen normal hour intracellular metabolite extraction extract-ms-7 pellet 40 mg liquid chromatography mass spectrometry Agilent C18 TTX Agilent QTOF XL Agilent MassDiscovery assay-name-ms-7 ms-data-7.mzml data_value MS metabolite identification IsoSolve MS-DT-ident isotopologue-distribution-analysis.txt diff --git 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a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/a_metabolite-profiling-nmr-assay.txt +++ /dev/null @@ -1,9 +0,0 @@ -Sample Name Factor Value[compound] Factor Value[dose] Factor Value[duration] Protocol REF Extract Name Protocol REF Parameter Value[magnetic field strength] Unit Parameter Value[nmr tube] Parameter Value[pulse sequence] NMR Assay Name Free Induction Decay File Protocol REF Parameter Value[nmr software] Data Transformation Name Derived Data File -culture-1-sample-0 dioxygen high hour intracellular metabolite extraction extract-nmr-metpro-0 1D 13C NMR spectroscopy for metabolite profiling 6 Tesla Brucker 14 mm Oscar CPMG assay-name-nmr-metpro-CPMG-1 nmr-data-topoHACO-DIPSY-8.nmrml NMR metabolite identification Batman NMR-metpro-DT-ident metpro-analysis.txt -culture-1-sample-1 dioxygen high hour intracellular metabolite extraction extract-nmr-metpro-2 1D 13C NMR spectroscopy for metabolite profiling 6 Tesla Brucker 14 mm Oscar CPMG assay-name-nmr-metpro-CPMG-3 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metpro-analysis.txt diff --git a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/i_investigation.txt b/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/i_investigation.txt deleted file mode 100644 index 357fd041a..000000000 --- a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/i_investigation.txt +++ /dev/null @@ -1,99 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name CHEBI EFO OBI PATO NCIBTaxon -Term Source File -Term Source Version -Term Source Description Chemical Entity of Biological Interest Experimental Factor Ontology Ontology for Biomedical Investigations Phenotype and Trait Ontology NCBI Taxonomy -INVESTIGATION -Investigation Identifier -Investigation Title -Investigation Description -Investigation Submission Date -Investigation Public Release Date -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation 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- "title": "Decyphering new cancer pathways with stable isotope resolved metabolomics in MCF7 cell lines" - } - ], - "studyDesignDescriptors": [ - { - "@id": "#ontology_annotation/ff482cf5-0cdf-4691-b941-2f588d4207bf", - "annotationValue": "intervention design", - "comments": [], - "termAccession": "http://purl.obolibrary.org/obo/OBI_0000115", - "termSource": "OBI" - }, - { - "@id": "#ontology_annotation/1116fad0-bd7e-4b42-b787-4e3378ea6a38", - "annotationValue": "stable isotope resolved metabolomics study", - "comments": [], - "termAccession": "http://purl.obolibrary.org/obo/MSIO_0000096", - "termSource": "" - } - ], - "submissionDate": "15/08/2021", - "title": "[U-13C6]-D-glucose labeling experiment in MCF7 cancer cell line", - "unitCategories": [] - } - ], - "submissionDate": "", - "title": "" -} \ No newline at end of file diff --git a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/s_13C-SIRM-study.txt b/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/s_13C-SIRM-study.txt deleted file mode 100644 index cf3545396..000000000 --- a/isa-cookbook/content/notebooks/output/MTBLS-XXXX-SIRM/s_13C-SIRM-study.txt +++ /dev/null @@ -1,9 +0,0 @@ -Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[cell line] Protocol REF Parameter Value[tracer molecule] Sample Name Factor Value[compound] Factor Value[dose] Factor Value[duration] -culture-1 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-1-sample-0 dioxygen high hour -culture-1 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-1-sample-1 dioxygen high hour -culture-1 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-1-sample-2 dioxygen high hour -culture-1 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-1-sample-3 dioxygen high hour -culture-2 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-2-sample-0 dioxygen normal hour -culture-2 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-2-sample-1 dioxygen normal hour -culture-2 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-2-sample-2 dioxygen normal hour -culture-2 Homo sapiens NCIBTaxon http://purl.obolibrary.org/obo/NCBITaxon_9606 MCF-7 cell culture and isotopic labeling 80% [1-13C1]-D-glucose + 20% [U-13C6]-D-glucose culture-2-sample-3 dioxygen normal hour diff --git a/isa-cookbook/content/notebooks/programmatic-rebuild-of-BII-S-3-with-ISA-API.ipynb b/isa-cookbook/content/notebooks/programmatic-rebuild-of-BII-S-3-with-ISA-API.ipynb index be0a4c54f..b486c614f 100644 --- a/isa-cookbook/content/notebooks/programmatic-rebuild-of-BII-S-3-with-ISA-API.ipynb +++ b/isa-cookbook/content/notebooks/programmatic-rebuild-of-BII-S-3-with-ISA-API.ipynb @@ -666,9 +666,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-api-py39", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-api-py39" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -680,7 +680,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb b/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb index 4c408f70f..e108c0b32 100644 --- a/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb +++ b/isa-cookbook/content/notebooks/querying-isa-with-graphql-and-sparql.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -31,7 +31,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -41,7 +41,7 @@ "from rdflib import Graph, Namespace\n", "\n", "from isatools.isajson import load\n", - "from isatools.model import set_context" + "from isatools.model.context import set_context" ] }, { @@ -53,7 +53,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62,11 +62,6 @@ " investigation = load(f)" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, { "cell_type": "markdown", "metadata": {}, @@ -76,17 +71,9 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['sample collection', 'nucleic acid extraction', 'reverse transcription', 'library construction', 'nucleic acid sequencing', 'data transformation']\n" - ] - } - ], + "outputs": [], "source": [ "query = \"\"\"\n", "{\n", @@ -117,7 +104,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -145,7 +132,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -165,12 +152,12 @@ "source": [ "## 6. Generate an RDF graph\n", "\n", - "Before we can generate a graph we need to create the proper namespaces and transform the `ld` variable into a string" + "Before we can generate a graph, we need to create the proper namespaces and transform the `ld` variable into a string" ] }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -196,17 +183,9 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['sample collection', 'nucleic acid extraction', 'reverse transcription', 'library construction', 'nucleic acid sequencing', 'data transformation']\n" - ] - } - ], + "outputs": [], "source": [ "query = \"\"\"\n", "PREFIX rdf: \n", @@ -237,7 +216,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -251,9 +230,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, - "nbformat_minor": 1 -} \ No newline at end of file + "nbformat_minor": 4 +} diff --git a/isa-cookbook/content/notebooks/reading-isa-tab-from-disk-exploring-and-validating.ipynb b/isa-cookbook/content/notebooks/reading-isa-tab-from-disk-exploring-and-validating.ipynb index 6622d8d92..6441bc442 100644 --- a/isa-cookbook/content/notebooks/reading-isa-tab-from-disk-exploring-and-validating.ipynb +++ b/isa-cookbook/content/notebooks/reading-isa-tab-from-disk-exploring-and-validating.ipynb @@ -29,7 +29,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -41,7 +41,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -60,9 +60,22 @@ }, { "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "[Errno 2] No such file or directory: './s_DO_transcriptome/i_DO_transcriptome.txt'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mos\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mjoin\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m./s_DO_transcriptome\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mi_DO_transcriptome.txt\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m fp:\n\u001b[1;32m 2\u001b[0m ISA \u001b[38;5;241m=\u001b[39m isatab\u001b[38;5;241m.\u001b[39mload(fp)\n", + "File \u001b[0;32m~/Documents/git/isa-api/venv/lib/python3.10/site-packages/IPython/core/interactiveshell.py:324\u001b[0m, in \u001b[0;36m_modified_open\u001b[0;34m(file, *args, **kwargs)\u001b[0m\n\u001b[1;32m 317\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m file \u001b[38;5;129;01min\u001b[39;00m {\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m2\u001b[39m}:\n\u001b[1;32m 318\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 319\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIPython won\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt let you open fd=\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfile\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m by default \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 320\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mas it is likely to crash IPython. If you know what you are doing, \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 321\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124myou can use builtins\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m open.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 322\u001b[0m )\n\u001b[0;32m--> 324\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mio_open\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: './s_DO_transcriptome/i_DO_transcriptome.txt'" + ] + } + ], "source": [ "with open(os.path.join('./s_DO_transcriptome', 'i_DO_transcriptome.txt')) as fp:\n", " ISA = isatab.load(fp)" @@ -334,7 +347,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -348,9 +361,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.0" + "version": "3.10.10" } }, "nbformat": 4, "nbformat_minor": 4 -} \ No newline at end of file +} diff --git a/isa-cookbook/content/notebooks/xomics.ipynb b/isa-cookbook/content/notebooks/xomics.ipynb index 33216529b..ba3a0f334 100644 --- a/isa-cookbook/content/notebooks/xomics.ipynb +++ b/isa-cookbook/content/notebooks/xomics.ipynb @@ -1,13996 +1,1578 @@ { - "cells": [ - { - "cell_type": "markdown", - "id": "extra-newman", - "metadata": {}, - "source": [ - "# Read related files\n", - "\n", - "Non-standardized metadata files\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 445, - "id": "divided-handling", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['.DS_Store', 'IDs']" - ] - }, - "execution_count": 445, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import os\n", - "input_dir = \"./isa_container/input_files\"\n", - "os.listdir(path = input_dir)" - ] - }, - { - "cell_type": "markdown", - "id": "technical-missouri", - "metadata": {}, - "source": [ - "## Sample identifiers from ACTION" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "valuable-relationship", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Data frame dimensions\n", - " (10, 5)\n", - "Column names\n", - " Index(['XOmicsPhenoID', 'XOmicsGenoID', 'XOmicsFamID', 'XOmicsMethylID',\n", - " 'XOmicsmetaboID'],\n", - " dtype='object')\n", - "Missing value counts\n", - " XOmicsPhenoID 0\n", - "XOmicsGenoID 0\n", - "XOmicsFamID 0\n", - "XOmicsMethylID 0\n", - "XOmicsmetaboID 0\n", - "dtype: int64\n" - ] - }, - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 446, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import pandas as pd\n", - "IDs_file_path = \"./isa_container/input_files/IDs/ACTIONdemonstrator_XOmics_IDs_fake.csv\"\n", - "IDs_df = pd.read_csv(IDs_file_path).iloc[:10,]\n", - "print(\"Data frame dimensions\\n\", IDs_df.shape)\n", - "print(\"Column names\\n\", IDs_df.columns)\n", - "print(\"Missing value counts\\n\", IDs_df.isna().sum())\n", - "IDs_df.head" - ] - }, - { - "cell_type": "markdown", - "id": "6a666efa", - "metadata": {}, - "source": [ - "# Create ISA object" - ] - }, - { - "cell_type": "code", - "execution_count": 447, - "id": "c7603953", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/Users/philippe/Documents/git/isa-api2/isa-api/isa-cookbook/content/notebooks'" - ] - }, - "execution_count": 447, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# print current directory\n", - "import numpy as np\n", - "import os\n", - "os.getcwd()" - ] - }, - { - "cell_type": "markdown", - "id": "appreciated-maryland", - "metadata": {}, - "source": [ - "## Investigation\n", - "\n", - "Create a new ISA object" - ] - }, - { - "cell_type": "code", - "execution_count": 450, - "id": "composite-central", - "metadata": {}, - "outputs": [], - "source": [ - "# create new investigation with single study\n", - "from isatools.model import *\n", - "investigation = Investigation()\n" - ] - }, - { - "cell_type": "code", - "execution_count": 452, - "id": "contemporary-threshold", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data'" - ] - }, - "execution_count": 452, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# define title\n", - "investigation.title = \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\"\n", - "investigation.title" - ] - }, - { - "cell_type": "code", - "execution_count": 401, - "id": "balanced-working", - "metadata": {}, - "outputs": [], - "source": [ - "investigation.description = \"Predict childhood aggression with multi-omics data and demonstrate the FAIRification process and data analysis of a multi-omics project\"\n", - "investigation.identifier = \"tbd\"" - ] - }, - { - "cell_type": "markdown", - "id": "computational-student", - "metadata": {}, - "source": [ - "## Study" - ] - }, - { - "cell_type": "code", - "execution_count": 402, - "id": "sticky-correction", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[isatools.model.Study(filename='', identifier='', title='', description='', submission_date='', public_release_date='', contacts=[], design_descriptors=[], publications=[], factors=[], protocols=[], assays=[], sources=[], samples=[], process_sequence=[], other_material=[], characteristic_categories=[], comments=[], units=[])]" - ] - }, - "execution_count": 402, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# add one study to investigation\n", - "investigation.studies.append(Study())\n", - "investigation.studies" - ] - }, - { - "cell_type": "markdown", - "id": "competitive-opinion", - "metadata": {}, - "source": [ - "According to MetaboLights help site, the title should ideally be the same as for a corresponding manuscript." - ] - }, - { - "cell_type": "code", - "execution_count": 403, - "id": "married-trinity", - "metadata": {}, - "outputs": [], - "source": [ - "investigation.studies[0].title = \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\"\n", - "investigation.studies[0].identifier = \"tbd\" # TODO: add identifier; update title\n", - "investigation.studies[0].filename = \"s_study.txt\"" - ] - }, - { - "cell_type": "code", - "execution_count": 404, - "id": "violent-memorial", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "isatools.model.Study(filename='s_study.txt', identifier='tbd', title='X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data', description='', submission_date='', public_release_date='', contacts=[], design_descriptors=[], publications=[], factors=[], protocols=[], assays=[], sources=[], samples=[], process_sequence=[], other_material=[], characteristic_categories=[], comments=[], units=[])" - ] - }, - "execution_count": 404, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "investigation.studies[0]" - ] - }, - { - "cell_type": "markdown", - "id": "alien-winter", - "metadata": {}, - "source": [ - "### Ontologies\n", - "\n", - "Ontologies can be searched e.g. at http://www.ontobee.org/ or https://www.ebi.ac.uk/ols/index.\n", - "\n", - "FAIR genomes lookups: https://github.com/fairgenomes/fairgenomes-semantic-model/tree/main/lookups" - ] - }, - { - "cell_type": "code", - "execution_count": 405, - "id": "considered-assault", - "metadata": {}, - "outputs": [], - "source": [ - "# ontologies\n", - "ontologies = {\n", - " \"afo\": OntologySource(\n", - " name = \"AFO\",\n", - " description = \"Allotrope Merged Ontology Suite\"),\n", - " \"chebi\": OntologySource(\n", - " name = \"CHEBI\",\n", - " description = \"Chemical Entities of Biological Interest\"),\n", - " \"chmo\": OntologySource(\n", - " name = \"CHMO\", \n", - " description = \"Chemical Methods Ontology\"),\n", - " \"edam\": OntologySource(\n", - " name = \"EDAM\", \n", - " description = \"Bioinformatics operations, data types, formats, identifiers and topics\"),\n", - " \"efo\": OntologySource(\n", - " name = \"EFO\", \n", - " description = \"Experimental Factor Ontology\"),\n", - " \"ero\": OntologySource(\n", - " name = \"eagle-i resource ontology\",\n", - " description = \"An ontology of research resources such as instruments, protocols, reagents, animal models and biospecimens\"),\n", - " \"maxo\": OntologySource(\n", - " name = \"MAXO\", \n", - " description = \"Medical Action Ontology\"),\n", - " \"msio\": OntologySource(\n", - " name = \"MSIO\",\n", - " description = \"Metabolite Standards Initiative Ontology\"),\n", - " \"ncbitaxon\": OntologySource(\n", - " name = \"NCBITAXON\", \n", - " description = \"NCBI organismal classification\"),\n", - " \"ncit\": OntologySource(\n", - " name = \"NCIT\", \n", - " description = \"NCI Thesaurus OBO Edition\"),\n", - " \"obi\": OntologySource(\n", - " name = \"OBI\", \n", - " description = \"Ontology for Biomedical Investigations\"),\n", - " \"pato\": OntologySource(\n", - " name = \"PATO\", \n", - " description = \"PATO - the Phenotype And Trait Ontology\"),\n", - " \"uberon\": OntologySource(\n", - " name = \"UBERON\", \n", - " description = \"Uber-anatomy ontology\")\n", - "}\n", - "# add ontologies to investigation\n", - "for o in ontologies.values():\n", - " investigation.ontology_source_references.append(o)" - ] - }, - { - "cell_type": "markdown", - "id": "fatal-johns", - "metadata": {}, - "source": [ - "### Protocols" - ] - }, - { - "cell_type": "markdown", - "id": "bronze-offer", - "metadata": {}, - "source": [ - "Note that the protocol used in the process to derive `sample` from `source` MUST be of type 'sample collection' (see https://isa-specs.readthedocs.io/en/latest/isatab.html#study-table-file). \n", - "\n", - "- ISA model source: https://github.com/ISA-tools/isa-api/blob/master/isatools/model.py" - ] - }, - { - "cell_type": "code", - "execution_count": 406, - "id": "personal-customer", - "metadata": {}, - "outputs": [], - "source": [ - "protocol_params = {\n", - " \"anatomical entity\": ProtocolParameter(\n", - " parameter_name = OntologyAnnotation(\n", - " term = \"anatomical entity\",\n", - " term_source = ontologies[\"uberon\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/UBERON_0001062\"))\n", - "}\n", - "# define sample collection protocol\n", - "sample_collection_protocol = Protocol(\n", - " name = \"sample collection\", \n", - " # see github.com/ISA-tools/isa-specs/blob/master/source/isatab.rst \n", - " # -> MUST be of type 'sample collection'\n", - " protocol_type = OntologyAnnotation(term = \"sample collection\"),\n", - " parameters = [protocol_params[\"anatomical entity\"]])\n", - "investigation.studies[0].protocols.append(sample_collection_protocol)" - ] - }, - { - "cell_type": "markdown", - "id": "excessive-reducing", - "metadata": {}, - "source": [ - "### Metabolomics\n", - "\n", - "See also https://ebi.ac.uk/metabolights/guides/Protocol/Protocol for protocols required for submission in MetaboLights, i.e. Sample collection, Extraction, Chromatography, Mass spectrometry, Data transformation, and Metabolite identification." - ] - }, - { - "cell_type": "markdown", - "id": "mysterious-movement", - "metadata": {}, - "source": [ - "### Study factors" - ] - }, - { - "cell_type": "code", - "execution_count": 407, - "id": "spare-supervisor", - "metadata": {}, - "outputs": [], - "source": [ - "# gender\n", - "studyfactor_gender = StudyFactor(\n", - " name = \"genotypic sex\", \n", - " factor_type = OntologyAnnotation( # Ontology source reference\n", - " term = \"genotypic sex\", # also used in FAIR genomes\n", - " term_source = ontologies[\"pato\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/PATO_0020000\"))\n", - "# female\n", - "factorvalue_female = FactorValue(\n", - " factor_name = studyfactor_gender, \n", - " value = OntologyAnnotation( # str or OntologyAnnotation\n", - " term = \"XX Genotype\", # also used in FAIR genomes\n", - " term_source = ontologies[\"ncit\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C45976\"))\n", - "# male\n", - "factorvalue_male = FactorValue(\n", - " factor_name = studyfactor_gender, \n", - " value = OntologyAnnotation( # str or OntologyAnnotation\n", - " term = \"XY Genotype\", # also used in FAIR genomes\n", - " term_source = ontologies[\"ncit\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C45977\"))" - ] - }, - { - "cell_type": "code", - "execution_count": 408, - "id": "every-exposure", - "metadata": {}, - "outputs": [], - "source": [ - "# agressive behaviour assessment - T-scores\n", - "studyfactor_aggression = StudyFactor(\n", - " name = \"aggression score\", \n", - " factor_type = OntologyAnnotation( \n", - " term = \"childhood aggressive behaviour measurement\", \n", - " term_source = ontologies[\"efo\"], \n", - " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0007663\"),\n", - " comments = [\n", - " Comment(name = \"T-score reference\",\n", - " value = \"Age- and sex-specific Aggressive Behaviour T-score as described in Hagenbeek et al. https://doi.org/10.3389/fpyst.2020.00165\")])\n", - "# T-score value\n", - "class FactorValueAggressionScore(FactorValue):\n", - " def __init__(self, \n", - " factor_name = studyfactor_aggression, \n", - " value = None,\n", - " unit = OntologyAnnotation( \n", - " term = \"T-score\", \n", - " term_source = ontologies[\"ncit\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C120401\"),\n", - " comments = None):\n", - " super().__init__(factor_name = factor_name, value = value, unit = unit, comments = comments)" - ] - }, - { - "cell_type": "markdown", - "id": "4300e488", - "metadata": {}, - "source": [ - "## Assays" - ] - }, - { - "cell_type": "markdown", - "id": "blocked-arctic", - "metadata": {}, - "source": [ - "### Genotyping" - ] - }, - { - "cell_type": "code", - "execution_count": 409, - "id": "material-ghost", - "metadata": {}, - "outputs": [], - "source": [ - "assay_genotype = Assay(filename = \"a_assay_genotype.txt\",\n", - " measurement_type = OntologyAnnotation(term = \"\", term_source = \"\", term_accession = \"\"),\n", - " technology_type = OntologyAnnotation(term = \"nucleotide sequencing\", term_source =\"\", term_accession = \"\"),\n", - " technology_platform = OntologyAnnotation(term = \"\", term_source = \"\", term_accession = \"\"))\n", - "# TODO: What sequencing plaform has been used?\n", - " " - ] - }, - { - "cell_type": "code", - "execution_count": 410, - "id": "efficient-tourist", - "metadata": {}, - "outputs": [], - "source": [ - "# define extraction and measurement protocols\n", - "dna_extraction_protocol = Protocol(\n", - " name = \"DNA extraction\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = \"DNA extraction\",\n", - " term_source = ontologies[\"obi\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/OBI_0000257\")) \n", - "# TODO: check type; compare to FAIR genomes\n", - "investigation.studies[0].protocols.append(dna_extraction_protocol)" - ] - }, - { - "cell_type": "code", - "execution_count": 411, - "id": "through-tactics", - "metadata": {}, - "outputs": [], - "source": [ - "genotype_profiling_protocol = Protocol(\n", - " name = \"genotype profiling\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = \"genotyping\",\n", - " term_source = ontologies[\"efo\"],\n", - " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0000750\")\n", - ")\n", - "investigation.studies[0].protocols.append(genotype_profiling_protocol)\n", - "# TODO: check type; compare to FAIR genomes" - ] - }, - { - "cell_type": "markdown", - "id": "devoted-crime", - "metadata": {}, - "source": [ - "### DNA methylation" - ] - }, - { - "cell_type": "code", - "execution_count": 412, - "id": "ultimate-clark", - "metadata": {}, - "outputs": [], - "source": [ - "assay_methylation = Assay(\n", - " filename = \"a_assay_methylation.txt\", \n", - " measurement_type = OntologyAnnotation(\n", - " term = \"Methylation Beta Value\",\n", - " term_source = ontologies[\"ncit\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C164051\"),\n", - " technology_type = OntologyAnnotation(\n", - " term = \"DNA methylation profiling by array assay\",\n", - " term_source = ontologies[\"obi\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/OBI_0001332\"),\n", - " technology_platform = OntologyAnnotation(\n", - " term = \"Illumina Infinium MethylationEPIC BeadChip\",\n", - " term_source = ontologies[\"obi\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/OBI_0002131\")\n", - " )\n" - ] - }, - { - "cell_type": "code", - "execution_count": 413, - "id": "sweet-supervisor", - "metadata": {}, - "outputs": [], - "source": [ - "# define extraction and measurement protocols\n", - "dna_extraction_protocol = Protocol(\n", - " name = \"DNA extraction\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = \"DNA extraction\",\n", - " term_source = ontologies[\"obi\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/OBI_0000257\")) \n", - "# TODO: check type; compare to FAIR genomes\n", - "investigation.studies[0].protocols.append(dna_extraction_protocol)" - ] - }, - { - "cell_type": "code", - "execution_count": 414, - "id": "cleared-routine", - "metadata": {}, - "outputs": [], - "source": [ - "methylation_profiling_protocol = Protocol(\n", - " name = \"methylation profiling\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = \"methylation profiling\",\n", - " term_source = ontologies[\"efo\"], \n", - " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0000751\"),\n", - "# components = [OntologyAnnotation(\n", - "# term = \"Illumina Infinium MethylationEPIC BeadChip\",\n", - "# term_source = obi, \n", - "# term_accession = \"http://purl.obolibrary.org/obo/OBI_0002131\")]\n", - " ) \n", - "investigation.studies[0].protocols.append(methylation_profiling_protocol)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "answering-sperm", - "metadata": {}, - "outputs": [], - "source": [ - "methylation_data_processing_protocol = Protocol(\n", - " name = \"methylation data processing protocol\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = \"Protocol\",\n", - " term_source = ontologies[\"edam\"], \n", - " term_accession = \"http://edamontology.org/data_2531\"),\n", - " description = \"Sinke, Lucy, van Iterson, Maarten, Cats, Davy, Slieker, Roderick, & Heijmans, Bas. (2019, July 11). DNAmArray: Streamlined workflow for the quality control, normalization, and analysis of Illumina methylation array data (Version 2.1). Zenodo. http://doi.org/10.5281/zenodo.3355292\",\n", - " uri = \"http://doi.org/10.5281/zenodo.3355292\")\n", - "investigation.studies[0].protocols.append(methylation_data_processing_protocol)" - ] - }, - { - "cell_type": "markdown", - "id": "unique-iraqi", - "metadata": {}, - "source": [ - "### Metabolomics" - ] - }, - { - "cell_type": "code", - "execution_count": 416, - "id": "digital-adelaide", - "metadata": {}, - "outputs": [], - "source": [ - "assay_metabolomics_amines = Assay(\n", - " filename = \"a_assay_metabolomics_amines.txt\",\n", - "\n", - " \n", - " measurement_type = OntologyAnnotation(\n", - " term = \"targeted metabolite profiling\",\n", - " term_source = ontologies[\"msio\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", - " \n", - " technology_type = OntologyAnnotation(\n", - " term = \"liquid chromatography-mass spectrometry\",\n", - " term_source = ontologies[\"chmo\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0000524\"))\n", - " \n", - "# sample_type = OntologyAnnotation(\n", - "# term = \"urine specimen\",\n", - "# term_source = ['obi'],\n", - "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", - " \n", - "\n", - "# \n", - "# technology_platform = OntologyAnnotation(\n", - "# term = \"\",\n", - "# term_source = ontologies[\"\"], \n", - "# term_accession = \"\")\n", - " # TODO: What exact platform/instrument has been used?" - ] - }, - { - "cell_type": "code", - "execution_count": 417, - "id": "enormous-wholesale", - "metadata": {}, - "outputs": [], - "source": [ - "assay_metabolomics_OA = Assay(\n", - " filename = \"a_assay_metabolomics_OA.txt\", \n", - " \n", - " measurement_type = OntologyAnnotation(\n", - " term = \"targeted metabolite profiling\",\n", - " term_source = ontologies[\"msio\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", - " \n", - " technology_type = OntologyAnnotation(\n", - " term = \"gas chromatography-mass spectrometry\",\n", - " term_source = ontologies[\"chmo\"]))\n", - " \n", - "# sample_type = OntologyAnnotation(\n", - "# term = \"urine specimen\",\n", - "# term_source = ['obi'],\n", - "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", - " \n", - " \n", - "# technology_platform = OntologyAnnotation(\n", - "# term = \"\",\n", - "# term_source = ontologies[\"\"], \n", - "# term_accession = \"\")\n", - " # TODO: What exact platform/instrument has been used?" - ] - }, - { - "cell_type": "code", - "execution_count": 418, - "id": "equipped-camel", - "metadata": {}, - "outputs": [], - "source": [ - "assay_metabolomics_steroids = Assay(\n", - " filename = \"a_assay_metabolomics_steroids.txt\", \n", - " \n", - " measurement_type = OntologyAnnotation(\n", - " term = \"targeted metabolite profiling\",\n", - " term_source = ontologies[\"msio\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", - " \n", - " technology_type = OntologyAnnotation(\n", - " term = \"high-performance liquid chromatography-mass spectrometry\",\n", - " term_source = ontologies[\"chmo\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0000796\"))\n", - " \n", - "# sample_type = OntologyAnnotation(\n", - "# term = \"urine specimen\",\n", - "# term_source = ['obi'],\n", - "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", - "\n", - "# technology_platform = OntologyAnnotation(\n", - "# term = \"\",\n", - "# term_source = ontologies[\"\"], \n", - "# term_accession = \"\")\n", - "# TODO: What exact platform/instrument has been used?" - ] - }, - { - "cell_type": "code", - "execution_count": 419, - "id": "systematic-channels", - "metadata": {}, - "outputs": [], - "source": [ - "urine_sampling_protocol = Protocol(\n", - " name = \"urine sampling\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'urine speciment collection',\n", - "# term_source = [''],\n", - " term_accession = 'http://snomed.info/id/57617002')\n", - ")\n", - "# TODO: is this useful a ontology?\n", - "\n", - "\n", - "investigation.studies[0].protocols.append(urine_sampling_protocol)" - ] - }, - { - "cell_type": "code", - "execution_count": 420, - "id": "greatest-suggestion", - "metadata": {}, - "outputs": [], - "source": [ - "extraction_metabolomics = Protocol(\n", - " name = \"Extraction\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'Extraction',\n", - " term_source = ontologies[\"ncit\"],\n", - " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C61575'),\n", - " parameters = [\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Post Extraction\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Derivatization\"))\n", - " ])" - ] - }, - { - "cell_type": "code", - "execution_count": 421, - "id": "center-recall", - "metadata": {}, - "outputs": [], - "source": [ - "chromatography = Protocol(\n", - " name = \"Chromatography\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'Chromatography',\n", - " term_source = ontologies[\"ncit\"],\n", - " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C16431'),\n", - " parameters = [\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Chromatography Instrument\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Column model\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Column type\"))\n", - " ])\n" - ] - }, - { - "cell_type": "code", - "execution_count": 422, - "id": "boolean-poultry", - "metadata": {}, - "outputs": [], - "source": [ - "labelling_metabolites = Protocol(\n", - " name = \"Labelling metabolites\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'Labelling',\n", - " term_source = ontologies[\"chmo\"],\n", - " term_accession = 'http://purl.obolibrary.org/obo/CHMO_0001675')\n", - " )" - ] - }, - { - "cell_type": "code", - "execution_count": 423, - "id": "responsible-stevens", - "metadata": {}, - "outputs": [], - "source": [ - "mass_spectrometry = Protocol(\n", - " name = \"Mass spectrometry\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'Mass spectrometry',\n", - " term_source = ontologies[\"ncit\"],\n", - " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C17156'),\n", - " parameters = [\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Scan polarity\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Scan m/z range\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Instrument\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Ion source\")),\n", - " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Mass analyzer\"))\n", - " ])" - ] - }, - { - "cell_type": "code", - "execution_count": 424, - "id": "incorporated-capital", - "metadata": {}, - "outputs": [], - "source": [ - "data_transformation = Protocol(\n", - " name = \"Data transformation\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'Data Transformation',\n", - " term_source = ontologies[\"ncit\"],\n", - " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C43582')\n", - " )" - ] - }, - { - "cell_type": "code", - "execution_count": 425, - "id": "minimal-miracle", - "metadata": {}, - "outputs": [], - "source": [ - "metabolite_identification = Protocol(\n", - " name = \"Metabolite identification\",\n", - " protocol_type = OntologyAnnotation(\n", - " term = 'peak identification',\n", - " term_source = ontologies[\"afo\"],\n", - " term_accession = 'http://purl.allotrope.erg/ontologies/process#AFP_0003618')\n", - " )\n", - "\n", - "# TODO: Is this the correct ontlogy (source)?" - ] - }, - { - "cell_type": "markdown", - "id": "confirmed-technique", - "metadata": {}, - "source": [ - "## ACTION samples\n", - "\n", - "Add samples to study and link to previously defined protocols and assays.\n", - "\n", - "For MetaboLights, sample information should include unique sample name, organism, organism part, sample type (control, QC, experimental sample), other descriptors as factors (age, gender)." - ] - }, - { - "cell_type": "code", - "execution_count": 426, - "id": "floating-summer", - "metadata": {}, - "outputs": [], - "source": [ - "for idx, row in IDs_df.iterrows(): \n", - " # add subjects (sources) \n", - " # TODO: issue - source should represent a source material such as urine, \n", - " # and sample a respective extract or similar\n", - " # check if source was already added already (rows can contain duplicate entries)\n", - " #is_new_source = True\n", - " source_name = row[\"XOmicsPhenoID\"]\n", - " source = next((src for src in investigation.studies[0].sources \n", - " if src.name == source_name), None)\n", - " if not source:\n", - " #is_new_source = False\n", - " # create new source for subject\n", - " source = Source(name = row[\"XOmicsPhenoID\"])\n", - " # Characteristics - Organism - should be included for Metabolights\n", - " # here, organism is defined per source, i.e. individual\n", - " source.characteristics.append(\n", - " Characteristic(\n", - " category = OntologyAnnotation(\n", - " term = \"organism\"), \n", - " # TODO: add term source and accession for category? would such information be lost in ISA-Tab?\n", - " value = OntologyAnnotation(\n", - " term = \"Homo sapiens\",\n", - " term_source = ontologies[\"ncbitaxon\"],\n", - " term_accession = \"http://purl.bioontology.org/ontology/NCBITAXON/9606\")))\n", - " # TODO: check if family ID should/should not be added / is required for analysis\n", - " source.characteristics.append(\n", - " Characteristic(category = \"family ID\",\n", - " value = row[\"XOmicsFamID\"]))\n", - " source.characteristics.append(\n", - " Characteristic(\n", - " category = OntologyAnnotation( \n", - " term = \"childhood aggressive behaviour measurement\", \n", - " term_source = ontologies[\"efo\"], \n", - " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0007663\"),\n", - " value = \"\", #tscore,\n", - " unit = OntologyAnnotation( \n", - " term = \"T-score\", \n", - " term_source = ontologies[\"ncit\"], \n", - " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C120401\")))\n", - " #source.factor_values.append(FactorValueAggressionScore(value = tscore))\n", - " \n", - " # add subject to study\n", - " investigation.studies[0].sources.append(source)\n", - " \n", - " # add samples - sample names need to be unique\n", - " # urine sample for metabolomics\n", - " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", - " # check if urine sample was already added to study\n", - " urine_sample_name = \"urine_{0}\".format(source_name)\n", - " urine_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == urine_sample_name), None)\n", - " if not urine_sample:\n", - " # create a new sample with unique name\n", - " urine_sample = Sample(\n", - " name = urine_sample_name, \n", - " derives_from = [source]) # the individual\n", - " # Characteristics - Organism part - should be included for Metabolights\n", - " # here, organism part is defined per sample\n", - " urine_sample.characteristics.append(\n", - " Characteristic(\n", - " category = OntologyAnnotation(term = \"organism part\"),\n", - " value = OntologyAnnotation(\n", - " term = \"urine\",\n", - " term_source = ontologies[\"uberon\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/UBERON_0001088\")))\n", - " # Characteristics - sample type - should be included for Metabolights \n", - " # i.e. control, QC, experimental sample\n", - " urine_sample.characteristics.append(\n", - " Characteristic(\n", - " category = \"sample type\", # TODO: could not find a term yet; sample type is not an ontological term, but required by MetaboLights\n", - " value = OntologyAnnotation(\n", - " term = \"experimental sample\",\n", - " term_source = ontologies[\"chmo\"],\n", - " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0002746\")))\n", - " # add urine sample to study\n", - " investigation.studies[0].samples.append(urine_sample)\n", - " \n", - " # check if urine sampling process exists for source\n", - " urine_p_name = \"urine_specimen_collection_process_{0}\".format(source.name)\n", - " urine_collection_process = next(\n", - " (prcs for prcs in investigation.studies[0].process_sequence \n", - " if prcs.name == urine_p_name), None)\n", - " if not urine_collection_process:\n", - " # define urine sampling process for this subject\n", - " urine_collection_process = Process(\n", - " name = urine_p_name, \n", - " executes_protocol = sample_collection_protocol,\n", - " parameter_values = [\n", - " ParameterValue(\n", - " category = protocol_params[\"anatomical entity\"], #ProtocolParameter \n", - " value = \"urine\")],\n", - " inputs = [source],\n", - " outputs = [urine_sample])\n", - " investigation.studies[0].process_sequence.append(urine_collection_process)\n", - " else:\n", - " # urine sampling process already exists for the source\n", - " # add urine sample to outputs of existing process\n", - " urine_collection_process.outputs.append(urine_sample)\n", - " \n", - " # add samples\n", - " # buccal swab sample for genotyping and DNA methylation arrays\n", - " if not pd.isna(row[\"XOmicsGenoID\"]) or not pd.isna(row[\"XOmicsMethylID\"]):\n", - " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", - " \n", - " buccal_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == buccal_sample_name), None)\n", - " \n", - " if not buccal_sample:\n", - " # create sample of buccal mucosa\n", - " buccal_sample = Sample(\n", - " name = buccal_sample_name, \n", - " derives_from = [source]) # same source as urine sample\n", - " buccal_sample.characteristics.append(\n", - " Characteristic(\n", - " category = OntologyAnnotation(term = \"organism part\"),\n", - " value = \"\"))\n", - " # TODO: add more characteristics - compare to urime sample\n", - " # add sample to study\n", - " investigation.studies[0].samples.append(buccal_sample) \n", - " \n", - " # check if buccal swab sampling process exists for source\n", - " # needs to be checked, because multiple samples can be derived from one source\n", - " buccal_p_name = \"buccal_specimen_collection_process_{0}\".format(source.name)\n", - " buccal_collection_process = next(\n", - " (prcs for prcs in investigation.studies[0].process_sequence \n", - " if prcs.name == buccal_p_name), None)\n", - " if not buccal_collection_process:\n", - " # define buccal sampling process for this subject\n", - " buccal_collection_process = Process(\n", - " name = buccal_p_name, \n", - " executes_protocol = sample_collection_protocol,\n", - " parameter_values = [\n", - " ParameterValue(\n", - " category = protocol_params[\"anatomical entity\"], #ProtocolParameter \n", - " value = \"buccal mucosa\")],\n", - " inputs = [source],\n", - " outputs = [buccal_sample]\n", - " )\n", - " investigation.studies[0].process_sequence.append(buccal_collection_process)\n", - " \n", - " else:\n", - " # buccal sampling process already exists for the source\n", - " # add buccal sample to outputs of existing process\n", - " buccal_collection_process.outputs.append(buccal_sample)\n", - " \n", - " # NOTE: adding extraction process at study level doesn seem to work\n", - " # causes sample to disappear from study file\n", - " \n", - " \n", - "\n", - " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", - " # dna_extraction_process = next(())\n", - " # assay_methylation.samples.append(buccal_sample) # first check if already added\n", - " # methylation_profiling_process = Process(\n", - " # name = \"methylation_profiling_{0}\".format(source.name),\n", - " # executes_protocol = methylation_profiling_protocol,\n", - " # inputs = [buccal_sample], \n", - " ## outputs = [buccal_dna])\n", - " " - ] - }, - { - "cell_type": "markdown", - "id": "decent-budapest", - "metadata": {}, - "source": [ - "Genotype assay" - ] - }, - { - "cell_type": "code", - "execution_count": 427, - "id": "honey-salon", - "metadata": {}, - "outputs": [], - "source": [ - "# add samples to genotype assay\n", - "for idx, row in IDs_df.iterrows(): \n", - " source_name = row[\"XOmicsPhenoID\"]\n", - " if not pd.isna(row[\"XOmicsGenoID\"]):\n", - " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", - " buccal_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == buccal_sample_name), None)\n", - " genotype_sample = next(\n", - " (smpl for smpl in assay_genotype.samples \n", - " if smpl.name == buccal_sample_name), None)\n", - " if not genotype_sample:\n", - " assay_genotype.samples.append(buccal_sample) # first check if already added\n", - " # define DNA as material extracted from buccal mucosa sample\n", - " # on study level, because the same DNA is used for genotyping AND DNA methylation profiling\n", - " # TODO: check if this works; could be that extraction has to be on assay level\n", - " # but Study object has process_sequence, i.e. this is technically possible \n", - " # define DNA material for this sample\n", - " # now trying on assay level\n", - " buccal_dna = Material(\n", - " name = \"buccal_DNA_{0}\".format(row[\"XOmicsGenoID\"]),\n", - " type_ = \"Extract Name\")\n", - " # define extraction process for buccal DNA\n", - " dna_extraction_process = Process(\n", - " name = \"DNA_extraction_{0}\".format(row[\"XOmicsGenoID\"]),\n", - " executes_protocol = dna_extraction_protocol,\n", - " inputs = [buccal_sample], \n", - " outputs = [buccal_dna])\n", - " \n", - "\n", - " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", - " # dna_extraction_process = next(())\n", - "\n", - " genotype_profiling_process = Process(\n", - " name = \"genotype_profiling_{0}\".format(row[\"XOmicsGenoID\"]),\n", - " executes_protocol = genotype_profiling_protocol,\n", - " inputs = [buccal_dna])\n", - " \n", - " plink(dna_extraction_process, genotype_profiling_process)\n", - " assay_genotype.process_sequence.append(dna_extraction_process) \n", - " assay_genotype.process_sequence.append(genotype_profiling_process) " - ] - }, - { - "cell_type": "code", - "execution_count": 428, - "id": "vietnamese-newspaper", - "metadata": {}, - "outputs": [], - "source": [ - "# add samples to methylation assay\n", - "for idx, row in IDs_df.iterrows(): \n", - " source_name = row[\"XOmicsPhenoID\"]\n", - " if not pd.isna(row[\"XOmicsMethylID\"]):\n", - " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", - " buccal_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == buccal_sample_name), None)\n", - " methylation_sample = next(\n", - " (smpl for smpl in assay_methylation.samples \n", - " if smpl.name == buccal_sample_name), None)\n", - " if not methylation_sample:\n", - " assay_methylation.samples.append(buccal_sample) # first check if already added\n", - " # define DNA as material extracted from buccal mucosa sample\n", - " # on study level, because the same DNA is used for genotyping AND DNA methylation profiling\n", - " # TODO: check if this works; could be that extraction has to be on assay level\n", - " # but Study object has process_sequence, i.e. this is technically possible \n", - " # define DNA material for this sample\n", - " # now trying on assay level\n", - " buccal_dna = Material(\n", - " name = \"buccal_DNA_{0}\".format(row[\"XOmicsMethylID\"]),\n", - " type_ = \"Extract Name\")\n", - " # define extraction process for buccal DNA\n", - " dna_extraction_process = Process(\n", - " name = \"DNA_extraction_{0}\".format(row[\"XOmicsMethylID\"]),\n", - " executes_protocol = dna_extraction_protocol,\n", - " inputs = [buccal_sample], \n", - " outputs = [buccal_dna])\n", - " \n", - "\n", - " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", - " # dna_extraction_process = next(())\n", - "\n", - " methylation_profiling_process = Process(\n", - " name = \"methylation_profiling_{0}\".format(row[\"XOmicsMethylID\"]),\n", - " executes_protocol = methylation_profiling_protocol,\n", - " inputs = [buccal_dna])\n", - " \n", - " plink(dna_extraction_process, methylation_profiling_process)\n", - " assay_methylation.process_sequence.append(dna_extraction_process) \n", - " assay_methylation.process_sequence.append(methylation_profiling_process) " - ] - }, - { - "cell_type": "markdown", - "id": "higher-trinidad", - "metadata": {}, - "source": [ - "Metabolomics assays" - ] - }, - { - "cell_type": "code", - "execution_count": 429, - "id": "residential-reservation", - "metadata": {}, - "outputs": [], - "source": [ - "# add samples, processes and datafiles to metabolomics Amines assay\n", - "\n", - "Assay = assay_metabolomics_amines\n", - "\n", - "# Define datafiles (not all may be relevant)\n", - "\n", - "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", - "\n", - "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", - "\n", - "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", - "\n", - "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Data Transformation Name\")\n", - "\n", - "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", - " \n", - "\n", - "# Loop over samples and add process to samples\n", - "for idx, row in IDs_df.iterrows():\n", - " source_name = row[\"XOmicsPhenoID\"]\n", - "# print(source_name)\n", - " if not pd.isna(row[\"XOmicsmetaboID\"]): \n", - " # print(row['XOmicsmetaboID'])\n", - " urine_sample_name = \"urine_{0}\".format(source_name)\n", - "# print(urine_sample_name)\n", - " urine_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == urine_sample_name), None)\n", - "\n", - " metabolomics_sample = next(\n", - " (smpl for smpl in Assay.samples \n", - " if smpl.name == urine_sample_name), None)\n", - " \n", - " if not metabolomics_sample:\n", - " \n", - " \n", - " \n", - " ## Extraction\n", - " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = OntologyAnnotation(term=\"1 uL borate buffer (pH 8.8) with AQC reagent\"))\n", - " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"AQC\")\n", - " \n", - " material_extract = Material(\n", - " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ = \"Extract Name\")\n", - " \n", - " extraction_process = Process(\n", - " executes_protocol=extraction_metabolomics, \n", - " parameter_values=[Post_extraction, Derivatization],\n", - " inputs = [urine_sample],\n", - " outputs = [material_extract])\n", - " \n", - " \n", - " ## Labelling\n", - " material_label = Material(\n", - " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ =\"Labeled Extract Name\")\n", - "\n", - " labelling_process = Process(\n", - " executes_protocol=labelling_metabolites,\n", - " inputs = [extraction_process.outputs[0]],\n", - " outputs = [material_label])\n", - " \n", - " \n", - " ## Chromatography\n", - "# separated_molecules = Material(\n", - "# name = \"separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", - "# type_ =\"Labeled Extract Name\")\n", - "# )\n", - " \n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent 1290 Infinity II\")\n", - " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"Accq-Tag Ultra column (waters + FURHTER SPECS?)\")\n", - " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"reverse phase\")\n", - "\n", - " chromatography_process = Process(\n", - " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = chromatography,\n", - " parameter_values = [instrument, column_model, column_type],\n", - " inputs = [labelling_process.outputs[0]],\n", - " outputs = []\n", - "# outputs = [separated_molecules]\n", - " )\n", - " \n", - " \n", - " ## Mass spectrometry\n", - " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"positive\")\n", - " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"5-2000?\")\n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"AB SCIEX Qtrap 6500\")\n", - " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"ESI\")\n", - " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"triple quadrupole linear ion trap\")\n", - " \n", - " mass_spectrometry_process = Process(\n", - " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol= mass_spectrometry,\n", - " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", - "# inputs = [separated_molecules],\n", - " inputs = [],\n", - " outputs = [raw_datafile]\n", - " )\n", - " \n", - " \n", - " ## Data transformation\n", - " data_transformation_process = Process(\n", - " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = data_transformation,\n", - " inputs = [raw_datafile],\n", - " outputs = [normalized_datafile, derived_spectral_data_file]\n", - " )\n", - " \n", - " \n", - " ## Metabolite identification\n", - " metabolite_identification_process = Process(\n", - " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = metabolite_identification,\n", - " inputs = [normalized_datafile],\n", - " outputs= [Data_Transformation_Name, MAF]\n", - " )\n", - " \n", - " \n", - " # Link processes\n", - " plink(extraction_process, labelling_process)\n", - " plink(labelling_process, chromatography_process)\n", - " plink(chromatography_process, mass_spectrometry_process)\n", - " plink(mass_spectrometry_process, data_transformation_process)\n", - " plink(data_transformation_process, metabolite_identification_process)\n", - " \n", - " \n", - " # Add samples, materials and data files to the amines assay\n", - " Assay.samples.append(urine_sample)\n", - " Assay.other_material.append(material_extract)\n", - " Assay.other_material.append(material_label)\n", - "# Assay.other_material.append(separated_molecules)\n", - " Assay.data_files.append(raw_datafile)\n", - " Assay.data_files.append(normalized_datafile)\n", - " Assay.data_files.append(derived_spectral_data_file)\n", - " Assay.data_files.append(Data_Transformation_Name) \n", - " Assay.data_files.append(MAF)\n", - " \n", - " \n", - " ## Add processes to the amines assay\n", - " Assay.process_sequence.append(extraction_process)\n", - " Assay.process_sequence.append(labelling_process)\n", - " Assay.process_sequence.append(chromatography_process)\n", - " Assay.process_sequence.append(mass_spectrometry_process)\n", - " Assay.process_sequence.append(data_transformation_process)\n", - " Assay.process_sequence.append(metabolite_identification_process)" - ] - }, - { - "cell_type": "code", - "execution_count": 430, - "id": "informal-paragraph", - "metadata": {}, - "outputs": [], - "source": [ - "# add samples, processes and datafiles to metabolomics OA assay\n", - "\n", - "Assay = assay_metabolomics_OA\n", - "\n", - "# Define datafiles (not all may be relevant)\n", - "\n", - "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", - "\n", - "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", - "\n", - "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", - "\n", - "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Data Transformation Name\")\n", - "\n", - "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", - " \n", - "\n", - "# Loop over samples and add process to samples\n", - "for idx, row in IDs_df.iterrows():\n", - " source_name = row[\"XOmicsPhenoID\"]\n", - "# print(source_name)\n", - " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", - "# print(row['XOmicsmetaboID'])\n", - " urine_sample_name = \"urine_{0}\".format(source_name)\n", - "# print(urine_sample_name)\n", - " urine_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == urine_sample_name), None)\n", - "\n", - " metabolomics_sample = next(\n", - " (smpl for smpl in Assay.samples \n", - " if smpl.name == urine_sample_name), None)\n", - " \n", - " if not metabolomics_sample:\n", - " Assay.samples.append(urine_sample)\n", - " \n", - " \n", - " ## Extraction\n", - " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = \"1 uL pyridine\")\n", - " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"oximation followed by silylation\")\n", - " \n", - " \n", - " \n", - " material_extract = Material(\n", - " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ = \"Extract Name\")\n", - " \n", - " extraction_process = Process(\n", - " executes_protocol=extraction_metabolomics, \n", - " parameter_values=[Post_extraction, Derivatization],\n", - " inputs = [urine_sample],\n", - " outputs = [material_extract])\n", - " \n", - " \n", - " ## Labelling\n", - " material_label = Material(\n", - " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ =\"Labeled Extract Name\")\n", - "\n", - " \n", - " labelling_process = Process(\n", - " executes_protocol=labelling_metabolites,\n", - " inputs = [extraction_process.outputs[0]],\n", - " outputs = [material_label])\n", - " \n", - " \n", - "# ## Chromatography\n", - "# separated_molecules = Material(\n", - "# name = \"separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", - "# type_ =\"Labeled Extract Name\")\n", - "# )\n", - " \n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent Technologies 7890A\")\n", - " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um\")\n", - " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"low polarity\")\n", - "\n", - " \n", - " chromatography_process = Process(\n", - " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = chromatography,\n", - " parameter_values = [instrument, column_model, column_type],\n", - " inputs = [labelling_process.outputs[0]], \n", - " outputs = [],\n", - "# outputs = [separated_molecules]\n", - " )\n", - " \n", - " ## Mass spectrometry\n", - " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"positive\")\n", - " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"50-500\")\n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL)\")\n", - " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"EI (70 eV)\")\n", - " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"single-quadrupole\")\n", - " \n", - " \n", - " mass_spectrometry_process = Process(\n", - " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol= mass_spectrometry,\n", - " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", - " inputs = [],\n", - "# inputs = [separated_molecules],\n", - " outputs = [raw_datafile]\n", - " )\n", - " \n", - " \n", - " ## Data transformation\n", - " data_transformation_process = Process(\n", - " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = data_transformation,\n", - " inputs = [raw_datafile],\n", - " outputs = [normalized_datafile, derived_spectral_data_file]\n", - " )\n", - " \n", - " ## Metabolite identification\n", - " metabolite_identification_process = Process(\n", - " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = metabolite_identification,\n", - " inputs = [normalized_datafile],\n", - " outputs= [Data_Transformation_Name, MAF]\n", - " )\n", - " \n", - "# ## Link processes\n", - " plink(extraction_process, labelling_process)\n", - " plink(labelling_process, chromatography_process)\n", - " plink(chromatography_process, mass_spectrometry_process)\n", - " plink(mass_spectrometry_process, data_transformation_process)\n", - " plink(data_transformation_process, metabolite_identification_process)\n", - " \n", - "# ## Add samples, materials and data files to the OA assay\n", - " Assay.other_material.append(material_extract)\n", - " Assay.other_material.append(material_label)\n", - "# Assay.other_material.append(separated_molecules)\n", - " Assay.data_files.append(raw_datafile)\n", - " Assay.data_files.append(normalized_datafile)\n", - " Assay.data_files.append(derived_spectral_data_file)\n", - " Assay.data_files.append(Data_Transformation_Name) \n", - " Assay.data_files.append(MAF)\n", - " \n", - "# ## Add processes to the OA assay\n", - " Assay.process_sequence.append(extraction_process)\n", - " Assay.process_sequence.append(labelling_process)\n", - " Assay.process_sequence.append(chromatography_process)\n", - " Assay.process_sequence.append(mass_spectrometry_process)\n", - " Assay.process_sequence.append(data_transformation_process)\n", - " Assay.process_sequence.append(metabolite_identification_process)" - ] - }, - { - "cell_type": "code", - "execution_count": 432, - "id": "silent-fever", - "metadata": {}, - "outputs": [], - "source": [ - "# add samples, processes and datafiles to metabolomics steroids assay\n", - "\n", - "Assay = assay_metabolomics_steroids\n", - "\n", - "# Define datafiles (not all may be relevant)\n", - "\n", - "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", - "\n", - "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", - "\n", - "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", - "\n", - "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Data Transformation Name\")\n", - "\n", - "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", - " \n", - "\n", - "# Loop over samples and add process to samples\n", - "for idx, row in IDs_df.iterrows():\n", - " source_name = row[\"XOmicsPhenoID\"]\n", - "# print(source_name)\n", - " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", - "# print(row['XOmicsmetaboID'])\n", - " urine_sample_name = \"urine_{0}\".format(source_name)\n", - "# print(urine_sample_name)\n", - " urine_sample = next(\n", - " (smpl for smpl in investigation.studies[0].samples \n", - " if smpl.name == urine_sample_name), None)\n", - "\n", - " metabolomics_sample = next(\n", - " (smpl for smpl in Assay.samples \n", - " if smpl.name == urine_sample_name), None)\n", - " \n", - " if not metabolomics_sample:\n", - " Assay.samples.append(urine_sample)\n", - " \n", - " \n", - " ## Extraction\n", - " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = \"1 uL filtered urine\")\n", - " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"NA\")\n", - "\n", - " \n", - " material_extract = Material(\n", - " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ = \"Extract Name\")\n", - " \n", - " extraction_process = Process(\n", - " executes_protocol=extraction_metabolomics, \n", - " parameter_values=[Post_extraction, Derivatization],\n", - " inputs = [urine_sample],\n", - " outputs = [material_extract])\n", - " \n", - " \n", - " ## Labelling\n", - " material_label = Material(\n", - " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " type_ =\"Labeled Extract Name\")\n", - "\n", - " \n", - " labelling_process = Process(\n", - " executes_protocol=labelling_metabolites,\n", - " inputs = [extraction_process.outputs[0]],\n", - " outputs = [material_label])\n", - " \n", - " \n", - " ## Chromatography\n", - "# separated_molecules = Material(\n", - "# name = \"new_separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", - "# type_ =\"Labeled Extract Name\") \n", - "# )\n", - " \n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent 1290\")\n", - " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"Acquity UPLC CSH C18 column (Waters)\")\n", - " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"reverse phase\")\n", - "\n", - " \n", - " chromatography_process = Process(\n", - " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = chromatography,\n", - " parameter_values = [instrument, column_model, column_type],\n", - " inputs = [labelling_process.outputs[0]], \n", - " outputs = []\n", - " #outputs = [separated_molecules]\n", - " )\n", - " \n", - " ## Mass spectrometry\n", - " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY?\")\n", - " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"5-3000?\")\n", - " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"Agilent 6460\")\n", - " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"ESI\")\n", - " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"triple quadrupole\")\n", - " \n", - " \n", - " mass_spectrometry_process = Process(\n", - " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol= mass_spectrometry,\n", - " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", - " # inputs = [separated_molecules],\n", - " inputs = [],\n", - " outputs = [raw_datafile]\n", - " )\n", - " \n", - " \n", - " ## Data transformation\n", - " data_transformation_process = Process(\n", - " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = data_transformation,\n", - " inputs = [raw_datafile],\n", - " outputs = [normalized_datafile, derived_spectral_data_file]\n", - " )\n", - " \n", - " ## Metabolite identification\n", - " metabolite_identification_process = Process(\n", - " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", - " executes_protocol = metabolite_identification,\n", - " inputs = [normalized_datafile],\n", - " outputs= [Data_Transformation_Name, MAF]\n", - " )\n", - " \n", - " ## Link processes\n", - " plink(extraction_process, labelling_process)\n", - " plink(labelling_process, chromatography_process)\n", - " plink(chromatography_process, mass_spectrometry_process)\n", - " plink(mass_spectrometry_process, data_transformation_process)\n", - " plink(data_transformation_process, metabolite_identification_process)\n", - " \n", - " ## Add samples, materials and data files to the steroids assay\n", - " Assay.other_material.append(material_extract)\n", - " Assay.other_material.append(material_label)\n", - " # Assay.other_material.append(separated_molecules)\n", - " Assay.data_files.append(raw_datafile)\n", - " Assay.data_files.append(normalized_datafile)\n", - " Assay.data_files.append(derived_spectral_data_file)\n", - " Assay.data_files.append(Data_Transformation_Name) \n", - " Assay.data_files.append(MAF)\n", - " \n", - " ## Add processes to the steroids assay\n", - " Assay.process_sequence.append(extraction_process)\n", - " Assay.process_sequence.append(labelling_process)\n", - " Assay.process_sequence.append(chromatography_process)\n", - " Assay.process_sequence.append(mass_spectrometry_process)\n", - " Assay.process_sequence.append(data_transformation_process)\n", - " Assay.process_sequence.append(metabolite_identification_process)" - ] - }, - { - "cell_type": "code", - "execution_count": 433, - "id": "given-beaver", - "metadata": {}, - "outputs": [], - "source": [ - "# add assays to study\n", - "investigation.studies[0].assays.append(assay_genotype)\n", - "investigation.studies[0].assays.append(assay_methylation)\n", - "investigation.studies[0].assays.append(assay_metabolomics_amines)\n", - "investigation.studies[0].assays.append(assay_metabolomics_OA)\n", - "investigation.studies[0].assays.append(assay_metabolomics_steroids)" - ] - }, - { - "cell_type": "markdown", - "id": "dramatic-webcam", - "metadata": {}, - "source": [ - "# Write ISA-Tab files" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "regular-palmer", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2021-12-01 22:51:43,707 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2995, 3000, 3005, 3010, 3015, 3020, 3025, 3030, 3035, 3040]\n", - "2021-12-01 22:51:43,709 [WARNING]: isatab.py(write_study_table_files:1194) >> [2997, 2996, 2995, 2999, 2998, 3002, 3001, 3000, 3004, 3003, 3007, 3006, 3005, 3009, 3008, 3012, 3011, 3010, 3014, 3013, 3017, 3016, 3015, 3019, 3018, 3022, 3021, 3020, 3024, 3023, 3027, 3026, 3025, 3029, 3028, 3032, 3031, 3030, 3034, 3033, 3037, 3036, 3035, 3039, 3038, 3042, 3041, 3040, 3044, 3043]\n", - "2021-12-01 22:51:43,709 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2995, 2997, 2996], [2995, 2999, 2998], [3000, 3002, 3001], [3000, 3004, 3003], [3005, 3009, 3008], [3005, 3007, 3006], [3010, 3012, 3011], [3010, 3014, 3013], [3015, 3017, 3016], [3015, 3019, 3018], [3020, 3022, 3021], [3020, 3024, 3023], [3025, 3027, 3026], [3025, 3029, 3028], [3030, 3034, 3033], [3030, 3032, 3031], [3035, 3037, 3036], [3035, 3039, 3038], [3040, 3042, 3041], [3040, 3044, 3043]]\n", - "2021-12-01 22:51:43,753 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2998, 3003, 3008, 3013, 3018, 3023, 3028, 3033, 3038, 3043]\n", - "2021-12-01 22:51:43,755 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2998, 3046, 3045, 3047], [3003, 3049, 3048, 3050], [3008, 3052, 3051, 3053], [3013, 3055, 3054, 3056], [3018, 3058, 3057, 3059], [3023, 3061, 3060, 3062], [3028, 3064, 3063, 3065], [3033, 3067, 3066, 3068], [3038, 3070, 3069, 3071], [3043, 3073, 3072, 3074]]\n", - "2021-12-01 22:51:43,757 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2998, 3046, 3045, 3047], [3003, 3049, 3048, 3050], [3008, 3052, 3051, 3053], [3013, 3055, 3054, 3056], [3018, 3058, 3057, 3059], [3023, 3061, 3060, 3062], [3028, 3064, 3063, 3065], [3033, 3067, 3066, 3068], [3038, 3070, 3069, 3071], [3043, 3073, 3072, 3074]]\n", - "2021-12-01 22:51:43,778 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2998, 3003, 3008, 3013, 3018, 3023, 3028, 3033, 3038, 3043]\n", - "2021-12-01 22:51:43,781 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2998, 3076, 3075, 3077], [3003, 3079, 3078, 3080], [3008, 3082, 3081, 3083], [3013, 3085, 3084, 3086], [3018, 3088, 3087, 3089], [3023, 3091, 3090, 3092], [3028, 3094, 3093, 3095], [3033, 3097, 3096, 3098], [3038, 3100, 3099, 3101], [3043, 3103, 3102, 3104]]\n", - "2021-12-01 22:51:43,782 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2998, 3076, 3075, 3077], [3003, 3079, 3078, 3080], [3008, 3082, 3081, 3083], [3013, 3085, 3084, 3086], [3018, 3088, 3087, 3089], [3023, 3091, 3090, 3092], [3028, 3094, 3093, 3095], [3033, 3097, 3096, 3098], [3038, 3100, 3099, 3101], [3043, 3103, 3102, 3104]]\n", - "2021-12-01 22:51:43,848 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2996, 3001, 3006, 3011, 3016, 3021, 3026, 3031, 3036, 3041]\n", - "2021-12-01 22:51:43,849 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3111, 3110, 3113, 3112, 3114, 3115, 3116, 3117], [3001, 3119, 3118, 3121, 3120, 3122, 3123, 3124, 3125], [3006, 3127, 3126, 3129, 3128, 3130, 3131, 3132, 3133], [3011, 3135, 3134, 3137, 3136, 3138, 3139, 3140, 3141], [3016, 3143, 3142, 3145, 3144, 3146, 3147, 3148, 3149], [3021, 3151, 3150, 3153, 3152, 3154, 3155, 3156, 3157], [3026, 3159, 3158, 3161, 3160, 3162, 3163, 3164, 3165], [3031, 3167, 3166, 3169, 3168, 3170, 3171, 3172, 3173], [3036, 3175, 3174, 3177, 3176, 3178, 3179, 3180, 3181], [3041, 3183, 3182, 3185, 3184, 3186, 3187, 3188, 3189]]\n", - "2021-12-01 22:51:43,851 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3111, 3110, 3113, 3112, 3114, 3115, 3116, 3117], [3001, 3119, 3118, 3121, 3120, 3122, 3123, 3124, 3125], [3006, 3127, 3126, 3129, 3128, 3130, 3131, 3132, 3133], [3011, 3135, 3134, 3137, 3136, 3138, 3139, 3140, 3141], [3016, 3143, 3142, 3145, 3144, 3146, 3147, 3148, 3149], [3021, 3151, 3150, 3153, 3152, 3154, 3155, 3156, 3157], [3026, 3159, 3158, 3161, 3160, 3162, 3163, 3164, 3165], [3031, 3167, 3166, 3169, 3168, 3170, 3171, 3172, 3173], [3036, 3175, 3174, 3177, 3176, 3178, 3179, 3180, 3181], [3041, 3183, 3182, 3185, 3184, 3186, 3187, 3188, 3189]]\n", - "2021-12-01 22:51:43,937 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2996, 3001, 3006, 3011, 3016, 3021, 3026, 3031, 3036, 3041]\n", - "2021-12-01 22:51:43,939 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3196, 3195, 3198, 3197, 3199, 3200, 3201, 3202], [3001, 3204, 3203, 3206, 3205, 3207, 3208, 3209, 3210], [3006, 3212, 3211, 3214, 3213, 3215, 3216, 3217, 3218], [3011, 3220, 3219, 3222, 3221, 3223, 3224, 3225, 3226], [3016, 3228, 3227, 3230, 3229, 3231, 3232, 3233, 3234], [3021, 3236, 3235, 3238, 3237, 3239, 3240, 3241, 3242], [3026, 3244, 3243, 3246, 3245, 3247, 3248, 3249, 3250], [3031, 3252, 3251, 3254, 3253, 3255, 3256, 3257, 3258], [3036, 3260, 3259, 3262, 3261, 3263, 3264, 3265, 3266], [3041, 3268, 3267, 3270, 3269, 3271, 3272, 3273, 3274]]\n", - "2021-12-01 22:51:43,941 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3196, 3195, 3198, 3197, 3199, 3200, 3201, 3202], [3001, 3204, 3203, 3206, 3205, 3207, 3208, 3209, 3210], [3006, 3212, 3211, 3214, 3213, 3215, 3216, 3217, 3218], [3011, 3220, 3219, 3222, 3221, 3223, 3224, 3225, 3226], [3016, 3228, 3227, 3230, 3229, 3231, 3232, 3233, 3234], [3021, 3236, 3235, 3238, 3237, 3239, 3240, 3241, 3242], [3026, 3244, 3243, 3246, 3245, 3247, 3248, 3249, 3250], [3031, 3252, 3251, 3254, 3253, 3255, 3256, 3257, 3258], [3036, 3260, 3259, 3262, 3261, 3263, 3264, 3265, 3266], [3041, 3268, 3267, 3270, 3269, 3271, 3272, 3273, 3274]]\n", - "2021-12-01 22:51:44,024 [INFO]: isatab.py(_all_end_to_end_paths:1131) >> [2996, 3001, 3006, 3011, 3016, 3021, 3026, 3031, 3036, 3041]\n", - "2021-12-01 22:51:44,025 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3281, 3280, 3283, 3282, 3284, 3285, 3286, 3287], [3001, 3289, 3288, 3291, 3290, 3292, 3293, 3294, 3295], [3006, 3297, 3296, 3299, 3298, 3300, 3301, 3302, 3303], [3011, 3305, 3304, 3307, 3306, 3308, 3309, 3310, 3311], [3016, 3313, 3312, 3315, 3314, 3316, 3317, 3318, 3319], [3021, 3321, 3320, 3323, 3322, 3324, 3325, 3326, 3327], [3026, 3329, 3328, 3331, 3330, 3332, 3333, 3334, 3335], [3031, 3337, 3336, 3339, 3338, 3340, 3341, 3342, 3343], [3036, 3345, 3344, 3347, 3346, 3348, 3349, 3350, 3351], [3041, 3353, 3352, 3355, 3354, 3356, 3357, 3358, 3359]]\n", - "2021-12-01 22:51:44,027 [INFO]: isatab.py(_longest_path_and_attrs:1091) >> [[2996, 3281, 3280, 3283, 3282, 3284, 3285, 3286, 3287], [3001, 3289, 3288, 3291, 3290, 3292, 3293, 3294, 3295], [3006, 3297, 3296, 3299, 3298, 3300, 3301, 3302, 3303], [3011, 3305, 3304, 3307, 3306, 3308, 3309, 3310, 3311], [3016, 3313, 3312, 3315, 3314, 3316, 3317, 3318, 3319], [3021, 3321, 3320, 3323, 3322, 3324, 3325, 3326, 3327], [3026, 3329, 3328, 3331, 3330, 3332, 3333, 3334, 3335], [3031, 3337, 3336, 3339, 3338, 3340, 3341, 3342, 3343], [3036, 3345, 3344, 3347, 3346, 3348, 3349, 3350, 3351], [3041, 3353, 3352, 3355, 3354, 3356, 3357, 3358, 3359]]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n" - ] - } - ], - "source": [ - "\n", - "from isatools import isatab\n", - "# create ISA files directory \n", - "out_dir = \"isa_template\"\n", - "if not os.path.isdir(out_dir):\n", - " os.makedirs(out_dir)\n", - "# write to ISA-Tab\n", - "isatab.dump(investigation, out_dir)\n", - "print()" - ] - }, - { - "cell_type": "code", - "execution_count": 435, - "id": "welcome-kitty", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"@id\": \"#investigation/5131975408\",\n", - " \"comments\": [],\n", - " \"description\": \"Predict childhood aggression with multi-omics data and demonstrate the FAIRification process and data analysis of a multi-omics project\",\n", - " \"identifier\": \"tbd\",\n", - " \"ontologySourceReferences\": [\n", - " {\n", - " \"@id\": \"#ontology/5133002736\",\n", - " \"comments\": [],\n", - " \"description\": \"Allotrope Merged Ontology Suite\",\n", - " \"file\": \"\",\n", - " \"name\": \"AFO\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5133003936\",\n", - " \"comments\": [],\n", - " \"description\": \"Chemical Entities of Biological Interest\",\n", - " \"file\": \"\",\n", - " \"name\": \"CHEBI\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5133003552\",\n", - " \"comments\": [],\n", - " \"description\": \"Chemical Methods Ontology\",\n", - " \"file\": \"\",\n", - " \"name\": \"CHMO\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134609760\",\n", - " \"comments\": [],\n", - " \"description\": \"Bioinformatics operations, data types, formats, identifiers and topics\",\n", - " \"file\": \"\",\n", - " \"name\": \"EDAM\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134607360\",\n", - " \"comments\": [],\n", - " \"description\": \"Experimental Factor Ontology\",\n", - " \"file\": \"\",\n", - " \"name\": \"EFO\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134130768\",\n", - " \"comments\": [],\n", - " \"description\": \"An ontology of research resources such as instruments, protocols, reagents, animal models and biospecimens\",\n", - " \"file\": \"\",\n", - " \"name\": \"eagle-i resource ontology\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134130912\",\n", - " \"comments\": [],\n", - " \"description\": \"Medical Action Ontology\",\n", - " \"file\": \"\",\n", - " \"name\": \"MAXO\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134130864\",\n", - " \"comments\": [],\n", - " \"description\": \"Metabolite Standards Initiative Ontology\",\n", - " \"file\": \"\",\n", - " \"name\": \"MSIO\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134130624\",\n", - " \"comments\": [],\n", - " \"description\": \"NCBI organismal classification\",\n", - " \"file\": \"\",\n", - " \"name\": \"NCBITAXON\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134131152\",\n", - " \"comments\": [],\n", - " \"description\": \"NCI Thesaurus OBO Edition\",\n", - " \"file\": \"\",\n", - " \"name\": \"NCIT\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#ontology/5134131104\",\n", - " \"comments\": [],\n", - " \"description\": \"Ontology for Biomedical Investigations\",\n", - 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" }\n", - " ],\n", - " \"protocols\": [\n", - " {\n", - " \"@id\": \"#protocol/5134609472\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"sample collection\",\n", - " \"parameters\": [\n", - " {\n", - " \"@id\": \"#parameter/5134610288\",\n", - " \"parameterName\": {\n", - " \"@id\": \"#annotation_value/832158af-e137-40f2-ae22-8b0397d8d8d5\",\n", - " \"annotationValue\": \"anatomical entity\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://purl.obolibrary.org/obo/UBERON_0001062\",\n", - " \"termSource\": \"UBERON\"\n", - " }\n", - " }\n", - " ],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/fe0cac02-b3bf-4156-9a82-f9a7bdfff388\",\n", - " \"annotationValue\": \"sample collection\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5132615984\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"DNA extraction\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/b49a1520-9758-42bb-b21d-27caf5b74315\",\n", - " \"annotationValue\": \"DNA extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://purl.obolibrary.org/obo/OBI_0000257\",\n", - " \"termSource\": \"OBI\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5134607888\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"genotype profiling\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/ef71f738-7112-4504-983f-6ec00437572d\",\n", - " \"annotationValue\": \"genotyping\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://www.ebi.ac.uk/efo/EFO_0000750\",\n", - " \"termSource\": \"EFO\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5132734720\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"DNA extraction\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/77363928-e00e-4861-bc81-c22a1518bfdc\",\n", - " \"annotationValue\": \"DNA extraction\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://purl.obolibrary.org/obo/OBI_0000257\",\n", - " \"termSource\": \"OBI\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5134647888\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"methylation profiling\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/0d5f6108-7e71-49d1-8ec8-280d359bbf84\",\n", - " \"annotationValue\": \"methylation profiling\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://www.ebi.ac.uk/efo/EFO_0000751\",\n", - " \"termSource\": \"EFO\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5130481920\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"Sinke, Lucy, van Iterson, Maarten, Cats, Davy, Slieker, Roderick, & Heijmans, Bas. (2019, July 11). DNAmArray: Streamlined workflow for the quality control, normalization, and analysis of Illumina methylation array data (Version 2.1). Zenodo. http://doi.org/10.5281/zenodo.3355292\",\n", - " \"name\": \"methylation data processing protocol\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/4b3671b2-d712-4629-b7fc-c26b3ba24182\",\n", - " \"annotationValue\": \"Protocol\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://edamontology.org/data_2531\",\n", - " \"termSource\": \"EDAM\"\n", - " },\n", - " \"uri\": \"http://doi.org/10.5281/zenodo.3355292\",\n", - " \"version\": \"\"\n", - " },\n", - " {\n", - " \"@id\": \"#protocol/5132735488\",\n", - " \"comments\": [],\n", - " \"components\": [],\n", - " \"description\": \"\",\n", - " \"name\": \"urine sampling\",\n", - " \"parameters\": [],\n", - " \"protocolType\": {\n", - " \"@id\": \"#annotation_value/caa25712-f8ae-4832-99de-9c5f1e6c5d1d\",\n", - " \"annotationValue\": \"urine speciment collection\",\n", - " \"comments\": [],\n", - " \"termAccession\": \"http://snomed.info/id/57617002\",\n", - " \"termSource\": \"\"\n", - " },\n", - " \"uri\": \"\",\n", - " \"version\": \"\"\n", - " }\n", - " ],\n", - " \"publicReleaseDate\": \"\",\n", - " \"publications\": [],\n", - " \"studyDesignDescriptors\": [],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\",\n", - " \"unitCategories\": []\n", - " }\n", - " ],\n", - " \"submissionDate\": \"\",\n", - " \"title\": \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\"\n", - "}\n" - ] - } - ], - "source": [ - "import json\n", - "from isatools.isajson import ISAJSONEncoder\n", - "print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "80b5d3ca", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "isa-api-py39", - "language": "python", - "name": "isa-api-py39" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 + "cells": [ + { + "cell_type": "markdown", + "id": "extra-newman", + "metadata": {}, + "source": [ + "# Read related files\n", + "\n", + "Non-standardized metadata files\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "divided-handling", + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "input_dir = \"./isa_container/input_files\"\n", + "os.listdir(path = input_dir)" + ] + }, + { + "cell_type": "markdown", + "id": "technical-missouri", + "metadata": {}, + "source": [ + "## Sample identifiers from ACTION" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "valuable-relationship", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "IDs_file_path = \"./isa_container/input_files/IDs/ACTIONdemonstrator_XOmics_IDs_fake.csv\"\n", + "IDs_df = pd.read_csv(IDs_file_path).iloc[:10,]\n", + "print(\"Data frame dimensions\\n\", IDs_df.shape)\n", + "print(\"Column names\\n\", IDs_df.columns)\n", + "print(\"Missing value counts\\n\", IDs_df.isna().sum())\n", + "IDs_df.head" + ] + }, + { + "cell_type": "markdown", + "id": "6a666efa", + "metadata": {}, + "source": [ + "# Create ISA object" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c7603953", + "metadata": {}, + "outputs": [], + "source": [ + "# print current directory\n", + "import numpy as np\n", + "import os\n", + "os.getcwd()" + ] + }, + { + "cell_type": "markdown", + "id": "appreciated-maryland", + "metadata": {}, + "source": [ + "## Investigation\n", + "\n", + "Create a new ISA object" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "composite-central", + "metadata": {}, + "outputs": [], + "source": [ + "# create new investigation with single study\n", + "from isatools.model import *\n", + "investigation = Investigation()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "contemporary-threshold", + "metadata": {}, + "outputs": [], + "source": [ + "# define title\n", + "investigation.title = \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\"\n", + "investigation.title" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "balanced-working", + "metadata": {}, + "outputs": [], + "source": [ + "investigation.description = \"Predict childhood aggression with multi-omics data and demonstrate the FAIRification process and data analysis of a multi-omics project\"\n", + "investigation.identifier = \"tbd\"" + ] + }, + { + "cell_type": "markdown", + "id": "computational-student", + "metadata": {}, + "source": [ + "## Study" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "sticky-correction", + "metadata": {}, + "outputs": [], + "source": [ + "# add one study to investigation\n", + "investigation.studies.append(Study())\n", + "investigation.studies" + ] + }, + { + "cell_type": "markdown", + "id": "competitive-opinion", + "metadata": {}, + "source": [ + "According to MetaboLights help site, the title should ideally be the same as for a corresponding manuscript." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "married-trinity", + "metadata": {}, + "outputs": [], + "source": [ + "investigation.studies[0].title = \"X-omics data analysis, integration and stewardship demonstrator dataset: NTR ACTION omics data\"\n", + "investigation.studies[0].identifier = \"tbd\" # TODO: add identifier; update title\n", + "investigation.studies[0].filename = \"s_study.txt\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "violent-memorial", + "metadata": {}, + "outputs": [], + "source": [ + "investigation.studies[0]" + ] + }, + { + "cell_type": "markdown", + "id": "alien-winter", + "metadata": {}, + "source": [ + "### Ontologies\n", + "\n", + "Ontologies can be searched e.g. at http://www.ontobee.org/ or https://www.ebi.ac.uk/ols/index.\n", + "\n", + "FAIR genomes lookups: https://github.com/fairgenomes/fairgenomes-semantic-model/tree/main/lookups" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "considered-assault", + "metadata": {}, + "outputs": [], + "source": [ + "# ontologies\n", + "ontologies = {\n", + " \"afo\": OntologySource(\n", + " name = \"AFO\",\n", + " description = \"Allotrope Merged Ontology Suite\"),\n", + " \"chebi\": OntologySource(\n", + " name = \"CHEBI\",\n", + " description = \"Chemical Entities of Biological Interest\"),\n", + " \"chmo\": OntologySource(\n", + " name = \"CHMO\", \n", + " description = \"Chemical Methods Ontology\"),\n", + " \"edam\": OntologySource(\n", + " name = \"EDAM\", \n", + " description = \"Bioinformatics operations, data types, formats, identifiers and topics\"),\n", + " \"efo\": OntologySource(\n", + " name = \"EFO\", \n", + " description = \"Experimental Factor Ontology\"),\n", + " \"ero\": OntologySource(\n", + " name = \"eagle-i resource ontology\",\n", + " description = \"An ontology of research resources such as instruments, protocols, reagents, animal models and biospecimens\"),\n", + " \"maxo\": OntologySource(\n", + " name = \"MAXO\", \n", + " description = \"Medical Action Ontology\"),\n", + " \"msio\": OntologySource(\n", + " name = \"MSIO\",\n", + " description = \"Metabolite Standards Initiative Ontology\"),\n", + " \"ncbitaxon\": OntologySource(\n", + " name = \"NCBITAXON\", \n", + " description = \"NCBI organismal classification\"),\n", + " \"ncit\": OntologySource(\n", + " name = \"NCIT\", \n", + " description = \"NCI Thesaurus OBO Edition\"),\n", + " \"obi\": OntologySource(\n", + " name = \"OBI\", \n", + " description = \"Ontology for Biomedical Investigations\"),\n", + " \"pato\": OntologySource(\n", + " name = \"PATO\", \n", + " description = \"PATO - the Phenotype And Trait Ontology\"),\n", + " \"uberon\": OntologySource(\n", + " name = \"UBERON\", \n", + " description = \"Uber-anatomy ontology\")\n", + "}\n", + "# add ontologies to investigation\n", + "for o in ontologies.values():\n", + " investigation.ontology_source_references.append(o)" + ] + }, + { + "cell_type": "markdown", + "id": "fatal-johns", + "metadata": {}, + "source": [ + "### Protocols" + ] + }, + { + "cell_type": "markdown", + "id": "bronze-offer", + "metadata": {}, + "source": [ + "Note that the protocol used in the process to derive `sample` from `source` MUST be of type 'sample collection' (see https://isa-specs.readthedocs.io/en/latest/isatab.html#study-table-file). \n", + "\n", + "- ISA model source: https://github.com/ISA-tools/isa-api/blob/master/isatools/model.py" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "personal-customer", + "metadata": {}, + "outputs": [], + "source": [ + "protocol_params = {\n", + " \"anatomical entity\": ProtocolParameter(\n", + " parameter_name = OntologyAnnotation(\n", + " term = \"anatomical entity\",\n", + " term_source = ontologies[\"uberon\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/UBERON_0001062\"))\n", + "}\n", + "# define sample collection protocol\n", + "sample_collection_protocol = Protocol(\n", + " name = \"sample collection\", \n", + " # see github.com/ISA-tools/isa-specs/blob/master/source/isatab.rst \n", + " # -> MUST be of type 'sample collection'\n", + " protocol_type = OntologyAnnotation(term = \"sample collection\"),\n", + " parameters = [protocol_params[\"anatomical entity\"]])\n", + "investigation.studies[0].protocols.append(sample_collection_protocol)" + ] + }, + { + "cell_type": "markdown", + "id": "excessive-reducing", + "metadata": {}, + "source": [ + "### Metabolomics\n", + "\n", + "See also https://ebi.ac.uk/metabolights/guides/Protocol/Protocol for protocols required for submission in MetaboLights, i.e. Sample collection, Extraction, Chromatography, Mass spectrometry, Data transformation, and Metabolite identification." + ] + }, + { + "cell_type": "markdown", + "id": "mysterious-movement", + "metadata": {}, + "source": [ + "### Study factors" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "spare-supervisor", + "metadata": {}, + "outputs": [], + "source": [ + "# gender\n", + "studyfactor_gender = StudyFactor(\n", + " name = \"genotypic sex\", \n", + " factor_type = OntologyAnnotation( # Ontology source reference\n", + " term = \"genotypic sex\", # also used in FAIR genomes\n", + " term_source = ontologies[\"pato\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/PATO_0020000\"))\n", + "# female\n", + "factorvalue_female = FactorValue(\n", + " factor_name = studyfactor_gender, \n", + " value = OntologyAnnotation( # str or OntologyAnnotation\n", + " term = \"XX Genotype\", # also used in FAIR genomes\n", + " term_source = ontologies[\"ncit\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C45976\"))\n", + "# male\n", + "factorvalue_male = FactorValue(\n", + " factor_name = studyfactor_gender, \n", + " value = OntologyAnnotation( # str or OntologyAnnotation\n", + " term = \"XY Genotype\", # also used in FAIR genomes\n", + " term_source = ontologies[\"ncit\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C45977\"))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "every-exposure", + "metadata": {}, + "outputs": [], + "source": [ + "# agressive behaviour assessment - T-scores\n", + "studyfactor_aggression = StudyFactor(\n", + " name = \"aggression score\", \n", + " factor_type = OntologyAnnotation( \n", + " term = \"childhood aggressive behaviour measurement\", \n", + " term_source = ontologies[\"efo\"], \n", + " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0007663\"),\n", + " comments = [\n", + " Comment(name = \"T-score reference\",\n", + " value = \"Age- and sex-specific Aggressive Behaviour T-score as described in Hagenbeek et al. https://doi.org/10.3389/fpyst.2020.00165\")])\n", + "# T-score value\n", + "class FactorValueAggressionScore(FactorValue):\n", + " def __init__(self, \n", + " factor_name = studyfactor_aggression, \n", + " value = None,\n", + " unit = OntologyAnnotation( \n", + " term = \"T-score\", \n", + " term_source = ontologies[\"ncit\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C120401\"),\n", + " comments = None):\n", + " super().__init__(factor_name = factor_name, value = value, unit = unit, comments = comments)" + ] + }, + { + "cell_type": "markdown", + "id": "4300e488", + "metadata": {}, + "source": [ + "## Assays" + ] + }, + { + "cell_type": "markdown", + "id": "blocked-arctic", + "metadata": {}, + "source": [ + "### Genotyping" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "material-ghost", + "metadata": {}, + "outputs": [], + "source": [ + "assay_genotype = Assay(filename = \"a_assay_genotype.txt\",\n", + " measurement_type = OntologyAnnotation(term = \"\", term_source = \"\", term_accession = \"\"),\n", + " technology_type = OntologyAnnotation(term = \"nucleotide sequencing\", term_source =\"\", term_accession = \"\"),\n", + " technology_platform = OntologyAnnotation(term = \"\", term_source = \"\", term_accession = \"\"))\n", + "# TODO: What sequencing plaform has been used?\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "efficient-tourist", + "metadata": {}, + "outputs": [], + "source": [ + "# define extraction and measurement protocols\n", + "dna_extraction_protocol = Protocol(\n", + " name = \"DNA extraction\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = \"DNA extraction\",\n", + " term_source = ontologies[\"obi\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/OBI_0000257\")) \n", + "# TODO: check type; compare to FAIR genomes\n", + "investigation.studies[0].protocols.append(dna_extraction_protocol)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "through-tactics", + "metadata": {}, + "outputs": [], + "source": [ + "genotype_profiling_protocol = Protocol(\n", + " name = \"genotype profiling\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = \"genotyping\",\n", + " term_source = ontologies[\"efo\"],\n", + " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0000750\")\n", + ")\n", + "investigation.studies[0].protocols.append(genotype_profiling_protocol)\n", + "# TODO: check type; compare to FAIR genomes" + ] + }, + { + "cell_type": "markdown", + "id": "devoted-crime", + "metadata": {}, + "source": [ + "### DNA methylation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ultimate-clark", + "metadata": {}, + "outputs": [], + "source": [ + "assay_methylation = Assay(\n", + " filename = \"a_assay_methylation.txt\", \n", + " measurement_type = OntologyAnnotation(\n", + " term = \"Methylation Beta Value\",\n", + " term_source = ontologies[\"ncit\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C164051\"),\n", + " technology_type = OntologyAnnotation(\n", + " term = \"DNA methylation profiling by array assay\",\n", + " term_source = ontologies[\"obi\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/OBI_0001332\"),\n", + " technology_platform = OntologyAnnotation(\n", + " term = \"Illumina Infinium MethylationEPIC BeadChip\",\n", + " term_source = ontologies[\"obi\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/OBI_0002131\")\n", + " )\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "sweet-supervisor", + "metadata": {}, + "outputs": [], + "source": [ + "# define extraction and measurement protocols\n", + "dna_extraction_protocol = Protocol(\n", + " name = \"DNA extraction\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = \"DNA extraction\",\n", + " term_source = ontologies[\"obi\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/OBI_0000257\")) \n", + "# TODO: check type; compare to FAIR genomes\n", + "investigation.studies[0].protocols.append(dna_extraction_protocol)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cleared-routine", + "metadata": {}, + "outputs": [], + "source": [ + "methylation_profiling_protocol = Protocol(\n", + " name = \"methylation profiling\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = \"methylation profiling\",\n", + " term_source = ontologies[\"efo\"], \n", + " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0000751\"),\n", + "# components = [OntologyAnnotation(\n", + "# term = \"Illumina Infinium MethylationEPIC BeadChip\",\n", + "# term_source = obi, \n", + "# term_accession = \"http://purl.obolibrary.org/obo/OBI_0002131\")]\n", + " ) \n", + "investigation.studies[0].protocols.append(methylation_profiling_protocol)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "answering-sperm", + "metadata": {}, + "outputs": [], + "source": [ + "methylation_data_processing_protocol = Protocol(\n", + " name = \"methylation data processing protocol\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = \"Protocol\",\n", + " term_source = ontologies[\"edam\"], \n", + " term_accession = \"http://edamontology.org/data_2531\"),\n", + " description = \"Sinke, Lucy, van Iterson, Maarten, Cats, Davy, Slieker, Roderick, & Heijmans, Bas. (2019, July 11). DNAmArray: Streamlined workflow for the quality control, normalization, and analysis of Illumina methylation array data (Version 2.1). Zenodo. http://doi.org/10.5281/zenodo.3355292\",\n", + " uri = \"http://doi.org/10.5281/zenodo.3355292\")\n", + "investigation.studies[0].protocols.append(methylation_data_processing_protocol)" + ] + }, + { + "cell_type": "markdown", + "id": "unique-iraqi", + "metadata": {}, + "source": [ + "### Metabolomics" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "digital-adelaide", + "metadata": {}, + "outputs": [], + "source": [ + "assay_metabolomics_amines = Assay(\n", + " filename = \"a_assay_metabolomics_amines.txt\",\n", + "\n", + " \n", + " measurement_type = OntologyAnnotation(\n", + " term = \"targeted metabolite profiling\",\n", + " term_source = ontologies[\"msio\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", + " \n", + " technology_type = OntologyAnnotation(\n", + " term = \"liquid chromatography-mass spectrometry\",\n", + " term_source = ontologies[\"chmo\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0000524\"))\n", + " \n", + "# sample_type = OntologyAnnotation(\n", + "# term = \"urine specimen\",\n", + "# term_source = ['obi'],\n", + "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", + " \n", + "\n", + "# \n", + "# technology_platform = OntologyAnnotation(\n", + "# term = \"\",\n", + "# term_source = ontologies[\"\"], \n", + "# term_accession = \"\")\n", + " # TODO: What exact platform/instrument has been used?" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "enormous-wholesale", + "metadata": {}, + "outputs": [], + "source": [ + "assay_metabolomics_OA = Assay(\n", + " filename = \"a_assay_metabolomics_OA.txt\", \n", + " \n", + " measurement_type = OntologyAnnotation(\n", + " term = \"targeted metabolite profiling\",\n", + " term_source = ontologies[\"msio\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", + " \n", + " technology_type = OntologyAnnotation(\n", + " term = \"gas chromatography-mass spectrometry\",\n", + " term_source = ontologies[\"chmo\"]))\n", + " \n", + "# sample_type = OntologyAnnotation(\n", + "# term = \"urine specimen\",\n", + "# term_source = ['obi'],\n", + "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", + " \n", + " \n", + "# technology_platform = OntologyAnnotation(\n", + "# term = \"\",\n", + "# term_source = ontologies[\"\"], \n", + "# term_accession = \"\")\n", + " # TODO: What exact platform/instrument has been used?" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "equipped-camel", + "metadata": {}, + "outputs": [], + "source": [ + "assay_metabolomics_steroids = Assay(\n", + " filename = \"a_assay_metabolomics_steroids.txt\", \n", + " \n", + " measurement_type = OntologyAnnotation(\n", + " term = \"targeted metabolite profiling\",\n", + " term_source = ontologies[\"msio\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/MSIO_0000100\"),\n", + " \n", + " technology_type = OntologyAnnotation(\n", + " term = \"high-performance liquid chromatography-mass spectrometry\",\n", + " term_source = ontologies[\"chmo\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0000796\"))\n", + " \n", + "# sample_type = OntologyAnnotation(\n", + "# term = \"urine specimen\",\n", + "# term_source = ['obi'],\n", + "# term_accession = \"http:/purl.obolibrary.org/obo/OBI_0000651\")\n", + "\n", + "# technology_platform = OntologyAnnotation(\n", + "# term = \"\",\n", + "# term_source = ontologies[\"\"], \n", + "# term_accession = \"\")\n", + "# TODO: What exact platform/instrument has been used?" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "systematic-channels", + "metadata": {}, + "outputs": [], + "source": [ + "urine_sampling_protocol = Protocol(\n", + " name = \"urine sampling\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'urine speciment collection',\n", + "# term_source = [''],\n", + " term_accession = 'http://snomed.info/id/57617002')\n", + ")\n", + "# TODO: is this useful a ontology?\n", + "\n", + "\n", + "investigation.studies[0].protocols.append(urine_sampling_protocol)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "greatest-suggestion", + "metadata": {}, + "outputs": [], + "source": [ + "extraction_metabolomics = Protocol(\n", + " name = \"Extraction\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'Extraction',\n", + " term_source = ontologies[\"ncit\"],\n", + " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C61575'),\n", + " parameters = [\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Post Extraction\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Derivatization\"))\n", + " ])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "center-recall", + "metadata": {}, + "outputs": [], + "source": [ + "chromatography = Protocol(\n", + " name = \"Chromatography\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'Chromatography',\n", + " term_source = ontologies[\"ncit\"],\n", + " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C16431'),\n", + " parameters = [\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Chromatography Instrument\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Column model\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Column type\"))\n", + " ])\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "boolean-poultry", + "metadata": {}, + "outputs": [], + "source": [ + "labelling_metabolites = Protocol(\n", + " name = \"Labelling metabolites\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'Labelling',\n", + " term_source = ontologies[\"chmo\"],\n", + " term_accession = 'http://purl.obolibrary.org/obo/CHMO_0001675')\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "responsible-stevens", + "metadata": {}, + "outputs": [], + "source": [ + "mass_spectrometry = Protocol(\n", + " name = \"Mass spectrometry\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'Mass spectrometry',\n", + " term_source = ontologies[\"ncit\"],\n", + " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C17156'),\n", + " parameters = [\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Scan polarity\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Scan m/z range\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Instrument\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Ion source\")),\n", + " ProtocolParameter(parameter_name=OntologyAnnotation(term = \"Mass analyzer\"))\n", + " ])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "incorporated-capital", + "metadata": {}, + "outputs": [], + "source": [ + "data_transformation = Protocol(\n", + " name = \"Data transformation\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'Data Transformation',\n", + " term_source = ontologies[\"ncit\"],\n", + " term_accession = 'http://purl.obolibrary.org/obo/NCIT_C43582')\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "minimal-miracle", + "metadata": {}, + "outputs": [], + "source": [ + "metabolite_identification = Protocol(\n", + " name = \"Metabolite identification\",\n", + " protocol_type = OntologyAnnotation(\n", + " term = 'peak identification',\n", + " term_source = ontologies[\"afo\"],\n", + " term_accession = 'http://purl.allotrope.erg/ontologies/process#AFP_0003618')\n", + " )\n", + "\n", + "# TODO: Is this the correct ontlogy (source)?" + ] + }, + { + "cell_type": "markdown", + "id": "confirmed-technique", + "metadata": {}, + "source": [ + "## ACTION samples\n", + "\n", + "Add samples to study and link to previously defined protocols and assays.\n", + "\n", + "For MetaboLights, sample information should include unique sample name, organism, organism part, sample type (control, QC, experimental sample), other descriptors as factors (age, gender)." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "floating-summer", + "metadata": {}, + "outputs": [], + "source": [ + "for idx, row in IDs_df.iterrows(): \n", + " # add subjects (sources) \n", + " # TODO: issue - source should represent a source material such as urine, \n", + " # and sample a respective extract or similar\n", + " # check if source was already added already (rows can contain duplicate entries)\n", + " #is_new_source = True\n", + " source_name = row[\"XOmicsPhenoID\"]\n", + " source = next((src for src in investigation.studies[0].sources \n", + " if src.name == source_name), None)\n", + " if not source:\n", + " #is_new_source = False\n", + " # create new source for subject\n", + " source = Source(name = row[\"XOmicsPhenoID\"])\n", + " # Characteristics - Organism - should be included for Metabolights\n", + " # here, organism is defined per source, i.e. individual\n", + " source.characteristics.append(\n", + " Characteristic(\n", + " category = OntologyAnnotation(\n", + " term = \"organism\"), \n", + " # TODO: add term source and accession for category? would such information be lost in ISA-Tab?\n", + " value = OntologyAnnotation(\n", + " term = \"Homo sapiens\",\n", + " term_source = ontologies[\"ncbitaxon\"],\n", + " term_accession = \"http://purl.bioontology.org/ontology/NCBITAXON/9606\")))\n", + " # TODO: check if family ID should/should not be added / is required for analysis\n", + " source.characteristics.append(\n", + " Characteristic(category = \"family ID\",\n", + " value = row[\"XOmicsFamID\"]))\n", + " source.characteristics.append(\n", + " Characteristic(\n", + " category = OntologyAnnotation( \n", + " term = \"childhood aggressive behaviour measurement\", \n", + " term_source = ontologies[\"efo\"], \n", + " term_accession = \"http://www.ebi.ac.uk/efo/EFO_0007663\"),\n", + " value = 0, #tscore,\n", + " unit = OntologyAnnotation( \n", + " term = \"T-score\", \n", + " term_source = ontologies[\"ncit\"], \n", + " term_accession = \"http://purl.obolibrary.org/obo/NCIT_C120401\")))\n", + " #source.factor_values.append(FactorValueAggressionScore(value = tscore))\n", + " \n", + " # add subject to study\n", + " investigation.studies[0].sources.append(source)\n", + " \n", + " # add samples - sample names need to be unique\n", + " # urine sample for metabolomics\n", + " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", + " # check if urine sample was already added to study\n", + " urine_sample_name = \"urine_{0}\".format(source_name)\n", + " urine_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == urine_sample_name), None)\n", + " if not urine_sample:\n", + " # create a new sample with unique name\n", + " urine_sample = Sample(\n", + " name = urine_sample_name, \n", + " derives_from = [source]) # the individual\n", + " # Characteristics - Organism part - should be included for Metabolights\n", + " # here, organism part is defined per sample\n", + " urine_sample.characteristics.append(\n", + " Characteristic(\n", + " category = OntologyAnnotation(term = \"organism part\"),\n", + " value = OntologyAnnotation(\n", + " term = \"urine\",\n", + " term_source = ontologies[\"uberon\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/UBERON_0001088\")))\n", + " # Characteristics - sample type - should be included for Metabolights \n", + " # i.e. control, QC, experimental sample\n", + " urine_sample.characteristics.append(\n", + " Characteristic(\n", + " category = \"sample type\", # TODO: could not find a term yet; sample type is not an ontological term, but required by MetaboLights\n", + " value = OntologyAnnotation(\n", + " term = \"experimental sample\",\n", + " term_source = ontologies[\"chmo\"],\n", + " term_accession = \"http://purl.obolibrary.org/obo/CHMO_0002746\")))\n", + " # add urine sample to study\n", + " investigation.studies[0].samples.append(urine_sample)\n", + " \n", + " # check if urine sampling process exists for source\n", + " urine_p_name = \"urine_specimen_collection_process_{0}\".format(source.name)\n", + " urine_collection_process = next(\n", + " (prcs for prcs in investigation.studies[0].process_sequence \n", + " if prcs.name == urine_p_name), None)\n", + " if not urine_collection_process:\n", + " # define urine sampling process for this subject\n", + " urine_collection_process = Process(\n", + " name = urine_p_name, \n", + " executes_protocol = sample_collection_protocol,\n", + " parameter_values = [\n", + " ParameterValue(\n", + " category = protocol_params[\"anatomical entity\"], #ProtocolParameter \n", + " value = \"urine\")],\n", + " inputs = [source],\n", + " outputs = [urine_sample])\n", + " investigation.studies[0].process_sequence.append(urine_collection_process)\n", + " else:\n", + " # urine sampling process already exists for the source\n", + " # add urine sample to outputs of existing process\n", + " urine_collection_process.outputs.append(urine_sample)\n", + " \n", + " # add samples\n", + " # buccal swab sample for genotyping and DNA methylation arrays\n", + " if not pd.isna(row[\"XOmicsGenoID\"]) or not pd.isna(row[\"XOmicsMethylID\"]):\n", + " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", + " \n", + " buccal_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == buccal_sample_name), None)\n", + " \n", + " if not buccal_sample:\n", + " # create sample of buccal mucosa\n", + " buccal_sample = Sample(\n", + " name = buccal_sample_name, \n", + " derives_from = [source]) # same source as urine sample\n", + " buccal_sample.characteristics.append(\n", + " Characteristic(\n", + " category = OntologyAnnotation(term = \"organism part\"),\n", + " value = \"\"))\n", + " # TODO: add more characteristics - compare to urime sample\n", + " # add sample to study\n", + " investigation.studies[0].samples.append(buccal_sample) \n", + " \n", + " # check if buccal swab sampling process exists for source\n", + " # needs to be checked, because multiple samples can be derived from one source\n", + " buccal_p_name = \"buccal_specimen_collection_process_{0}\".format(source.name)\n", + " buccal_collection_process = next(\n", + " (prcs for prcs in investigation.studies[0].process_sequence \n", + " if prcs.name == buccal_p_name), None)\n", + " if not buccal_collection_process:\n", + " # define buccal sampling process for this subject\n", + " buccal_collection_process = Process(\n", + " name = buccal_p_name, \n", + " executes_protocol = sample_collection_protocol,\n", + " parameter_values = [\n", + " ParameterValue(\n", + " category = protocol_params[\"anatomical entity\"], #ProtocolParameter \n", + " value = \"buccal mucosa\")],\n", + " inputs = [source],\n", + " outputs = [buccal_sample]\n", + " )\n", + " investigation.studies[0].process_sequence.append(buccal_collection_process)\n", + " \n", + " else:\n", + " # buccal sampling process already exists for the source\n", + " # add buccal sample to outputs of existing process\n", + " buccal_collection_process.outputs.append(buccal_sample)\n", + " \n", + " # NOTE: adding extraction process at study level doesn seem to work\n", + " # causes sample to disappear from study file\n", + " \n", + " \n", + "\n", + " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", + " # dna_extraction_process = next(())\n", + " # assay_methylation.samples.append(buccal_sample) # first check if already added\n", + " # methylation_profiling_process = Process(\n", + " # name = \"methylation_profiling_{0}\".format(source.name),\n", + " # executes_protocol = methylation_profiling_protocol,\n", + " # inputs = [buccal_sample], \n", + " ## outputs = [buccal_dna])\n", + " " + ] + }, + { + "cell_type": "markdown", + "id": "decent-budapest", + "metadata": {}, + "source": [ + "Genotype assay" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "honey-salon", + "metadata": {}, + "outputs": [], + "source": [ + "# add samples to genotype assay\n", + "for idx, row in IDs_df.iterrows(): \n", + " source_name = row[\"XOmicsPhenoID\"]\n", + " if not pd.isna(row[\"XOmicsGenoID\"]):\n", + " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", + " buccal_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == buccal_sample_name), None)\n", + " genotype_sample = next(\n", + " (smpl for smpl in assay_genotype.samples \n", + " if smpl.name == buccal_sample_name), None)\n", + " if not genotype_sample:\n", + " assay_genotype.samples.append(buccal_sample) # first check if already added\n", + " # define DNA as material extracted from buccal mucosa sample\n", + " # on study level, because the same DNA is used for genotyping AND DNA methylation profiling\n", + " # TODO: check if this works; could be that extraction has to be on assay level\n", + " # but Study object has process_sequence, i.e. this is technically possible \n", + " # define DNA material for this sample\n", + " # now trying on assay level\n", + " buccal_dna = Material(\n", + " name = \"buccal_DNA_{0}\".format(row[\"XOmicsGenoID\"]),\n", + " type_ = \"Extract Name\")\n", + " # define extraction process for buccal DNA\n", + " dna_extraction_process = Process(\n", + " name = \"DNA_extraction_{0}\".format(row[\"XOmicsGenoID\"]),\n", + " executes_protocol = dna_extraction_protocol,\n", + " inputs = [buccal_sample], \n", + " outputs = [buccal_dna])\n", + " \n", + "\n", + " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", + " # dna_extraction_process = next(())\n", + "\n", + " genotype_profiling_process = Process(\n", + " name = \"genotype_profiling_{0}\".format(row[\"XOmicsGenoID\"]),\n", + " executes_protocol = genotype_profiling_protocol,\n", + " inputs = [buccal_dna])\n", + " \n", + " plink(dna_extraction_process, genotype_profiling_process)\n", + " assay_genotype.process_sequence.append(dna_extraction_process) \n", + " assay_genotype.process_sequence.append(genotype_profiling_process) " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "vietnamese-newspaper", + "metadata": {}, + "outputs": [], + "source": [ + "# add samples to methylation assay\n", + "for idx, row in IDs_df.iterrows(): \n", + " source_name = row[\"XOmicsPhenoID\"]\n", + " if not pd.isna(row[\"XOmicsMethylID\"]):\n", + " buccal_sample_name = \"buccal_mucosa_{0}\".format(source_name)\n", + " buccal_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == buccal_sample_name), None)\n", + " methylation_sample = next(\n", + " (smpl for smpl in assay_methylation.samples \n", + " if smpl.name == buccal_sample_name), None)\n", + " if not methylation_sample:\n", + " assay_methylation.samples.append(buccal_sample) # first check if already added\n", + " # define DNA as material extracted from buccal mucosa sample\n", + " # on study level, because the same DNA is used for genotyping AND DNA methylation profiling\n", + " # TODO: check if this works; could be that extraction has to be on assay level\n", + " # but Study object has process_sequence, i.e. this is technically possible \n", + " # define DNA material for this sample\n", + " # now trying on assay level\n", + " buccal_dna = Material(\n", + " name = \"buccal_DNA_{0}\".format(row[\"XOmicsMethylID\"]),\n", + " type_ = \"Extract Name\")\n", + " # define extraction process for buccal DNA\n", + " dna_extraction_process = Process(\n", + " name = \"DNA_extraction_{0}\".format(row[\"XOmicsMethylID\"]),\n", + " executes_protocol = dna_extraction_protocol,\n", + " inputs = [buccal_sample], \n", + " outputs = [buccal_dna])\n", + " \n", + "\n", + " #if not pd.isna(row[\"XOmicsMethylID\"]):\n", + " # dna_extraction_process = next(())\n", + "\n", + " methylation_profiling_process = Process(\n", + " name = \"methylation_profiling_{0}\".format(row[\"XOmicsMethylID\"]),\n", + " executes_protocol = methylation_profiling_protocol,\n", + " inputs = [buccal_dna])\n", + " \n", + " plink(dna_extraction_process, methylation_profiling_process)\n", + " assay_methylation.process_sequence.append(dna_extraction_process) \n", + " assay_methylation.process_sequence.append(methylation_profiling_process) " + ] + }, + { + "cell_type": "markdown", + "id": "higher-trinidad", + "metadata": {}, + "source": [ + "Metabolomics assays" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "residential-reservation", + "metadata": {}, + "outputs": [], + "source": [ + "# add samples, processes and datafiles to metabolomics Amines assay\n", + "\n", + "Assay = assay_metabolomics_amines\n", + "\n", + "# Define datafiles (not all may be relevant)\n", + "\n", + "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", + "\n", + "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", + "\n", + "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", + "\n", + "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Derived Spectral Data File\")\n", + "\n", + "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", + " \n", + "\n", + "# Loop over samples and add process to samples\n", + "for idx, row in IDs_df.iterrows():\n", + " source_name = row[\"XOmicsPhenoID\"]\n", + "# print(source_name)\n", + " if not pd.isna(row[\"XOmicsmetaboID\"]): \n", + " # print(row['XOmicsmetaboID'])\n", + " urine_sample_name = \"urine_{0}\".format(source_name)\n", + "# print(urine_sample_name)\n", + " urine_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == urine_sample_name), None)\n", + "\n", + " metabolomics_sample = next(\n", + " (smpl for smpl in Assay.samples \n", + " if smpl.name == urine_sample_name), None)\n", + " \n", + " if not metabolomics_sample:\n", + " \n", + " \n", + " \n", + " ## Extraction\n", + " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = OntologyAnnotation(term=\"1 uL borate buffer (pH 8.8) with AQC reagent\"))\n", + " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"AQC\")\n", + " \n", + " material_extract = Material(\n", + " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ = \"Extract Name\")\n", + " \n", + " extraction_process = Process(\n", + " executes_protocol=extraction_metabolomics, \n", + " parameter_values=[Post_extraction, Derivatization],\n", + " inputs = [urine_sample],\n", + " outputs = [material_extract])\n", + " \n", + " \n", + " ## Labelling\n", + " material_label = Material(\n", + " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ =\"Labeled Extract Name\")\n", + "\n", + " labelling_process = Process(\n", + " executes_protocol=labelling_metabolites,\n", + " inputs = [extraction_process.outputs[0]],\n", + " outputs = [material_label])\n", + " \n", + " \n", + " ## Chromatography\n", + "# separated_molecules = Material(\n", + "# name = \"separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", + "# type_ =\"Labeled Extract Name\")\n", + "# )\n", + " \n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent 1290 Infinity II\")\n", + " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"Accq-Tag Ultra column (waters + FURHTER SPECS?)\")\n", + " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"reverse phase\")\n", + "\n", + " chromatography_process = Process(\n", + " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = chromatography,\n", + " parameter_values = [instrument, column_model, column_type],\n", + " inputs = [labelling_process.outputs[0]],\n", + " outputs = []\n", + "# outputs = [separated_molecules]\n", + " )\n", + " \n", + " \n", + " ## Mass spectrometry\n", + " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"positive\")\n", + " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"5-2000?\")\n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"AB SCIEX Qtrap 6500\")\n", + " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"ESI\")\n", + " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"triple quadrupole linear ion trap\")\n", + " \n", + " mass_spectrometry_process = Process(\n", + " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol= mass_spectrometry,\n", + " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", + "# inputs = [separated_molecules],\n", + " inputs = [],\n", + " outputs = [raw_datafile]\n", + " )\n", + " \n", + " \n", + " ## Data transformation\n", + " data_transformation_process = Process(\n", + " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = data_transformation,\n", + " inputs = [raw_datafile],\n", + " outputs = [normalized_datafile, derived_spectral_data_file]\n", + " )\n", + " \n", + " \n", + " ## Metabolite identification\n", + " metabolite_identification_process = Process(\n", + " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = metabolite_identification,\n", + " inputs = [normalized_datafile,derived_spectral_data_file],\n", + " outputs= [Data_Transformation_Name, MAF]\n", + " )\n", + " \n", + " \n", + " # Link processes\n", + " plink(extraction_process, labelling_process)\n", + " plink(labelling_process, chromatography_process)\n", + " plink(chromatography_process, mass_spectrometry_process)\n", + " plink(mass_spectrometry_process, data_transformation_process)\n", + " plink(data_transformation_process, metabolite_identification_process)\n", + " \n", + " \n", + " # Add samples, materials and data files to the amines assay\n", + " Assay.samples.append(urine_sample)\n", + " Assay.other_material.append(material_extract)\n", + " Assay.other_material.append(material_label)\n", + "# Assay.other_material.append(separated_molecules)\n", + " Assay.data_files.append(raw_datafile)\n", + " Assay.data_files.append(normalized_datafile)\n", + " Assay.data_files.append(derived_spectral_data_file)\n", + " Assay.data_files.append(Data_Transformation_Name) \n", + " Assay.data_files.append(MAF)\n", + " \n", + " \n", + " ## Add processes to the amines assay\n", + " Assay.process_sequence.append(extraction_process)\n", + " Assay.process_sequence.append(labelling_process)\n", + " Assay.process_sequence.append(chromatography_process)\n", + " Assay.process_sequence.append(mass_spectrometry_process)\n", + " Assay.process_sequence.append(data_transformation_process)\n", + " Assay.process_sequence.append(metabolite_identification_process)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "informal-paragraph", + "metadata": {}, + "outputs": [], + "source": [ + "# add samples, processes and datafiles to metabolomics OA assay\n", + "\n", + "Assay = assay_metabolomics_OA\n", + "\n", + "# Define datafiles (not all may be relevant)\n", + "\n", + "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", + "\n", + "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", + "\n", + "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", + "\n", + "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Derived Spectral Data File\")\n", + "\n", + "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", + " \n", + "\n", + "# Loop over samples and add process to samples\n", + "for idx, row in IDs_df.iterrows():\n", + " source_name = row[\"XOmicsPhenoID\"]\n", + "# print(source_name)\n", + " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", + "# print(row['XOmicsmetaboID'])\n", + " urine_sample_name = \"urine_{0}\".format(source_name)\n", + "# print(urine_sample_name)\n", + " urine_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == urine_sample_name), None)\n", + "\n", + " metabolomics_sample = next(\n", + " (smpl for smpl in Assay.samples \n", + " if smpl.name == urine_sample_name), None)\n", + " \n", + " if not metabolomics_sample:\n", + " Assay.samples.append(urine_sample)\n", + " \n", + " \n", + " ## Extraction\n", + " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = \"1 uL pyridine\")\n", + " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"oximation followed by silylation\")\n", + " \n", + " \n", + " \n", + " material_extract = Material(\n", + " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ = \"Extract Name\")\n", + " \n", + " extraction_process = Process(\n", + " executes_protocol=extraction_metabolomics, \n", + " parameter_values=[Post_extraction, Derivatization],\n", + " inputs = [urine_sample],\n", + " outputs = [material_extract])\n", + " \n", + " \n", + " ## Labelling\n", + " material_label = Material(\n", + " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ =\"Labeled Extract Name\")\n", + "\n", + " \n", + " labelling_process = Process(\n", + " executes_protocol=labelling_metabolites,\n", + " inputs = [extraction_process.outputs[0]],\n", + " outputs = [material_label])\n", + " \n", + " \n", + "# ## Chromatography\n", + "# separated_molecules = Material(\n", + "# name = \"separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", + "# type_ =\"Labeled Extract Name\")\n", + "# )\n", + " \n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent Technologies 7890A\")\n", + " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"HP-5MS UI (5% Phenyl Methyl Silox), 30 m x 0.25 m ID column with a film thickness of 25 um\")\n", + " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"low polarity\")\n", + "\n", + " \n", + " chromatography_process = Process(\n", + " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = chromatography,\n", + " parameter_values = [instrument, column_model, column_type],\n", + " inputs = [labelling_process.outputs[0]], \n", + " outputs = [],\n", + "# outputs = [separated_molecules]\n", + " )\n", + " \n", + " ## Mass spectrometry\n", + " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"positive\")\n", + " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"50-500\")\n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"Agilent Technologies mass selective detector (MSD 5975C) and MultiPurpose Sampler (MPS, MXY016-02A, GERSTEL)\")\n", + " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"EI (70 eV)\")\n", + " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"single-quadrupole\")\n", + " \n", + " \n", + " mass_spectrometry_process = Process(\n", + " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol= mass_spectrometry,\n", + " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", + " inputs = [],\n", + "# inputs = [separated_molecules],\n", + " outputs = [raw_datafile]\n", + " )\n", + " \n", + " \n", + " ## Data transformation\n", + " data_transformation_process = Process(\n", + " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = data_transformation,\n", + " inputs = [raw_datafile],\n", + " outputs = [normalized_datafile, derived_spectral_data_file]\n", + " )\n", + " \n", + " ## Metabolite identification\n", + " metabolite_identification_process = Process(\n", + " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = metabolite_identification,\n", + " inputs = [normalized_datafile,derived_spectral_data_file],\n", + " outputs= [Data_Transformation_Name, MAF]\n", + " )\n", + " \n", + "# ## Link processes\n", + " plink(extraction_process, labelling_process)\n", + " plink(labelling_process, chromatography_process)\n", + " plink(chromatography_process, mass_spectrometry_process)\n", + " plink(mass_spectrometry_process, data_transformation_process)\n", + " plink(data_transformation_process, metabolite_identification_process)\n", + " \n", + "# ## Add samples, materials and data files to the OA assay\n", + " Assay.other_material.append(material_extract)\n", + " Assay.other_material.append(material_label)\n", + "# Assay.other_material.append(separated_molecules)\n", + " Assay.data_files.append(raw_datafile)\n", + " Assay.data_files.append(normalized_datafile)\n", + " Assay.data_files.append(derived_spectral_data_file)\n", + " Assay.data_files.append(Data_Transformation_Name) \n", + " Assay.data_files.append(MAF)\n", + " \n", + "# ## Add processes to the OA assay\n", + " Assay.process_sequence.append(extraction_process)\n", + " Assay.process_sequence.append(labelling_process)\n", + " Assay.process_sequence.append(chromatography_process)\n", + " Assay.process_sequence.append(mass_spectrometry_process)\n", + " Assay.process_sequence.append(data_transformation_process)\n", + " Assay.process_sequence.append(metabolite_identification_process)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "silent-fever", + "metadata": {}, + "outputs": [], + "source": [ + "# add samples, processes and datafiles to metabolomics steroids assay\n", + "\n", + "Assay = assay_metabolomics_steroids\n", + "\n", + "# Define datafiles (not all may be relevant)\n", + "\n", + "raw_datafile = DataFile(filename=\"link/to/raw/data\", label=\"Raw Spectral Data File\")\n", + "\n", + "normalized_datafile = DataFile(filename=\"link/to/normalized_data\", label=\"Normalization Name\")\n", + "\n", + "derived_spectral_data_file = DataFile(filename=\"link/to/spectral_file\", label=\"Derived Spectral Data File\")\n", + "\n", + "Data_Transformation_Name = DataFile(filename=\"link/to/data_transformation_name\", label=\"Derived Spectral Data File\")\n", + "\n", + "MAF = DataFile(filename=\"link/to/MAF\", label=\"Metabolite Assignment File\")\n", + " \n", + "\n", + "# Loop over samples and add process to samples\n", + "for idx, row in IDs_df.iterrows():\n", + " source_name = row[\"XOmicsPhenoID\"]\n", + "# print(source_name)\n", + " if not pd.isna(row[\"XOmicsmetaboID\"]):\n", + "# print(row['XOmicsmetaboID'])\n", + " urine_sample_name = \"urine_{0}\".format(source_name)\n", + "# print(urine_sample_name)\n", + " urine_sample = next(\n", + " (smpl for smpl in investigation.studies[0].samples \n", + " if smpl.name == urine_sample_name), None)\n", + "\n", + " metabolomics_sample = next(\n", + " (smpl for smpl in Assay.samples \n", + " if smpl.name == urine_sample_name), None)\n", + " \n", + " if not metabolomics_sample:\n", + " Assay.samples.append(urine_sample)\n", + " \n", + " \n", + " ## Extraction\n", + " Post_extraction = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Post Extraction\")), value = \"1 uL filtered urine\")\n", + " Derivatization = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Derivatization\")), value = \"NA\")\n", + "\n", + " \n", + " material_extract = Material(\n", + " name = \"extract_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ = \"Extract Name\")\n", + " \n", + " extraction_process = Process(\n", + " executes_protocol=extraction_metabolomics, \n", + " parameter_values=[Post_extraction, Derivatization],\n", + " inputs = [urine_sample],\n", + " outputs = [material_extract])\n", + " \n", + " \n", + " ## Labelling\n", + " material_label = Material(\n", + " name =\"labeled_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " type_ =\"Labeled Extract Name\")\n", + "\n", + " \n", + " labelling_process = Process(\n", + " executes_protocol=labelling_metabolites,\n", + " inputs = [extraction_process.outputs[0]],\n", + " outputs = [material_label])\n", + " \n", + " \n", + " ## Chromatography\n", + "# separated_molecules = Material(\n", + "# name = \"new_separated_molecules_{0}\".format(row[\"XOmicsmetaboID\"],\n", + "# type_ =\"Labeled Extract Name\") \n", + "# )\n", + " \n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Chromatography Instrument\")), value = \"Agilent 1290\")\n", + " column_model = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column model\")), value = \"Acquity UPLC CSH C18 column (Waters)\")\n", + " column_type = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Column type\")), value = \"reverse phase\")\n", + "\n", + " \n", + " chromatography_process = Process(\n", + " name = \"chromatography_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = chromatography,\n", + " parameter_values = [instrument, column_model, column_type],\n", + " inputs = [labelling_process.outputs[0]], \n", + " outputs = []\n", + " #outputs = [separated_molecules]\n", + " )\n", + " \n", + " ## Mass spectrometry\n", + " scan_polarity = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan polarity\")), value = \"switching positive and negative ion mode !! MAYBE SERPARATE INTO NEGATIVE AND POSITIVE ASSAY?\")\n", + " scan_range = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Scan m/z range\")), value = \"5-3000?\")\n", + " instrument = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Instrument\")), value = \"Agilent 6460\")\n", + " ion_source = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Ion source\")), value = \"ESI\")\n", + " mass_analyzer = ParameterValue(category = ProtocolParameter(parameter_name=OntologyAnnotation(term=\"Mass Analyzer\")), value = \"triple quadrupole\")\n", + " \n", + " \n", + " mass_spectrometry_process = Process(\n", + " name = \"mass_spectrometry_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol= mass_spectrometry,\n", + " parameter_values = [scan_polarity, scan_range, instrument, ion_source, mass_analyzer],\n", + " # inputs = [separated_molecules],\n", + " inputs = [],\n", + " outputs = [raw_datafile]\n", + " )\n", + " \n", + " \n", + " ## Data transformation\n", + " data_transformation_process = Process(\n", + " name = \"data_transformation_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = data_transformation,\n", + " inputs = [raw_datafile],\n", + " outputs = [normalized_datafile, derived_spectral_data_file]\n", + " )\n", + " \n", + " ## Metabolite identification\n", + " metabolite_identification_process = Process(\n", + " name = \"metabolite_identification_{0}\".format(row[\"XOmicsmetaboID\"]),\n", + " executes_protocol = metabolite_identification,\n", + " inputs = [normalized_datafile,derived_spectral_data_file],\n", + " outputs= [Data_Transformation_Name, MAF]\n", + " )\n", + " \n", + " ## Link processes\n", + " plink(extraction_process, labelling_process)\n", + " plink(labelling_process, chromatography_process)\n", + " plink(chromatography_process, mass_spectrometry_process)\n", + " plink(mass_spectrometry_process, data_transformation_process)\n", + " plink(data_transformation_process, metabolite_identification_process)\n", + " \n", + " ## Add samples, materials and data files to the steroids assay\n", + " Assay.other_material.append(material_extract)\n", + " Assay.other_material.append(material_label)\n", + " # Assay.other_material.append(separated_molecules)\n", + " Assay.data_files.append(raw_datafile)\n", + " Assay.data_files.append(normalized_datafile)\n", + " Assay.data_files.append(derived_spectral_data_file)\n", + " Assay.data_files.append(Data_Transformation_Name) \n", + " Assay.data_files.append(MAF)\n", + " \n", + " ## Add processes to the steroids assay\n", + " Assay.process_sequence.append(extraction_process)\n", + " Assay.process_sequence.append(labelling_process)\n", + " Assay.process_sequence.append(chromatography_process)\n", + " Assay.process_sequence.append(mass_spectrometry_process)\n", + " Assay.process_sequence.append(data_transformation_process)\n", + " Assay.process_sequence.append(metabolite_identification_process)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "given-beaver", + "metadata": {}, + "outputs": [], + "source": [ + "# add assays to study\n", + "investigation.studies[0].assays.append(assay_genotype)\n", + "investigation.studies[0].assays.append(assay_methylation)\n", + "investigation.studies[0].assays.append(assay_metabolomics_amines)\n", + "investigation.studies[0].assays.append(assay_metabolomics_OA)\n", + "investigation.studies[0].assays.append(assay_metabolomics_steroids)" + ] + }, + { + "cell_type": "markdown", + "id": "dramatic-webcam", + "metadata": {}, + "source": [ + "# Write ISA-Tab files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "regular-palmer", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "from isatools import isatab\n", + "# create ISA files directory \n", + "out_dir = \"isa_template\"\n", + "if not os.path.isdir(out_dir):\n", + " os.makedirs(out_dir)\n", + "# write to ISA-Tab\n", + "isatab.dump(investigation, out_dir)\n", + "print()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "welcome-kitty", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "from isatools.isajson import ISAJSONEncoder\n", + "print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 }