From 9c45d0aa50ceb998976ce9915e1c4b426f018b89 Mon Sep 17 00:00:00 2001 From: Shakira <180181413+ShakiraSA@users.noreply.github.com> Date: Tue, 3 Feb 2026 11:51:33 +0100 Subject: [PATCH 1/4] Removing [METHOD] block Removing [METHOD] block from the title as this also appears on the platform --- docs/methods/cell_titer_fluor.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/methods/cell_titer_fluor.json b/docs/methods/cell_titer_fluor.json index d2c4c8d1..2a5257c1 100644 --- a/docs/methods/cell_titer_fluor.json +++ b/docs/methods/cell_titer_fluor.json @@ -1,6 +1,6 @@ { "id": "cell_titer_fluor", - "method": "[METHOD]: Cell Titer Fluor", + "method": "Cell Titer Fluor", "issue_number": 136, "name_of_the_method_content": "Cell Titer Fluor", "method_description_content": "A Non-Lytic Fluorescence Assay That Measures the Relative Number of Viable Cells in Culture", @@ -20,4 +20,4 @@ "regulatory_question_content": "Q1", "case_study_content": "thyroid", "timestamp": "2025-09-29T13:44:38.644368Z" -} \ No newline at end of file +} From 4378f0600eca5c02799a4a714d04b6b0e7a7354f Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 3 Feb 2026 10:51:42 +0000 Subject: [PATCH 2/4] Updated service meta-data collection --- cap/methods_index.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cap/methods_index.json b/cap/methods_index.json index 7ea869e2..bdc24fa7 100644 --- a/cap/methods_index.json +++ b/cap/methods_index.json @@ -45,7 +45,7 @@ }, "cell_titer_fluor": { "id": "cell_titer_fluor", - "method": "[METHOD]: Cell Titer Fluor", + "method": "Cell Titer Fluor", "issue_number": 136, "sop": "", "method_name_content": "Cell Titer Fluor", From e0771f121b3b5dd2fb5ebb7040250cc3b4c80424 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 3 Feb 2026 10:51:47 +0000 Subject: [PATCH 3/4] Generate service documentation from JSON files --- docs/service/aop-builder.md | 19 ++++----- docs/service/aopsuite.md | 21 ++++------ docs/service/aopwiki.md | 24 +++++------- docs/service/aopwikiapi.md | 18 +++------ docs/service/arrayanalysis.md | 22 ++++------- docs/service/biomodels.md | 19 ++++----- docs/service/biotransformer.md | 21 ++++------ docs/service/bmdexpress_3.md | 46 ++++++++++------------ docs/service/bridgedb.md | 30 ++++++-------- docs/service/cdk.md | 22 +++++------ docs/service/cdkdepict.md | 24 +++++------- docs/service/celldesigner.md | 19 ++++----- docs/service/comptox.md | 17 +++----- docs/service/copasi.md | 19 ++++----- docs/service/cplogd.md | 21 ++++------ docs/service/danish_qsar_database.md | 50 +++++++++++------------- docs/service/decimer.md | 25 +++++------- docs/service/dsld.md | 18 ++++----- docs/service/ema_documents.md | 17 +++----- docs/service/endocrine_disruptome.md | 46 ++++++++++------------ docs/service/fairdomhub.md | 17 +++----- docs/service/fairspace.md | 17 +++----- docs/service/farmacokompas.md | 17 +++----- docs/service/flame.md | 21 ++++------ docs/service/google.md | 18 ++++----- docs/service/gscholar.md | 18 ++++----- docs/service/jrc_data_catalogue.md | 17 +++----- docs/service/llemy.md | 32 +++++++-------- docs/service/mct8-dock.md | 30 ++++++-------- docs/service/molaopanalyser.md | 49 +++++++++++------------ docs/service/oecd_qsar_toolbox.md | 25 +++++------- docs/service/ontox_physiological_maps.md | 20 ++++------ docs/service/oppbk_model.md | 18 +++------ docs/service/opsin.md | 21 ++++------ docs/service/oqt_assistant.md | 36 +++++++---------- docs/service/qaop_app.md | 21 ++++------ docs/service/qsprpred.md | 24 +++++------- docs/service/r_odaf.md | 44 ++++++++++----------- docs/service/sombie.md | 21 ++++------ docs/service/sysrev.md | 20 ++++------ docs/service/toxtemp_assistant.md | 36 +++++++---------- docs/service/txg_mapr.md | 21 ++++------ docs/service/vhp_glossary.md | 18 ++++----- docs/service/wikibase.md | 25 +++++------- docs/service/wikipathways_aop.md | 29 ++++++-------- docs/service/xploreaop.md | 23 +++++------ 46 files changed, 455 insertions(+), 681 deletions(-) diff --git a/docs/service/aop-builder.md b/docs/service/aop-builder.md index 522c99c5..b1cb91c1 100644 --- a/docs/service/aop-builder.md +++ b/docs/service/aop-builder.md @@ -1,19 +1,13 @@ - # AOP-Builder - + A tool that supports Adverse Outcome Pathway (AOP) development by extracting key scientific entities and their relationships from literature. - -**Main Webpage:** [https://crebuilder.vhp4safety.nl](https://crebuilder.vhp4safety.nl) - -**Tool Webpage:** [https://crebuilder.vhp4safety.nl](https://crebuilder.vhp4safety.nl) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,15 +36,16 @@ A tool that supports Adverse Outcome Pathway (AOP) development by extracting key } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://crebuilder.vhp4safety.nl](https://crebuilder.vhp4safety.nl) +* Development Cloud: [https://crebuilder.vhp4safety.nl](https://crebuilder.vhp4safety.nl) * Login Required: Not available diff --git a/docs/service/aopsuite.md b/docs/service/aopsuite.md index 509f38ee..921495d6 100644 --- a/docs/service/aopsuite.md +++ b/docs/service/aopsuite.md @@ -1,20 +1,14 @@ - # AOP-Suite - + A web-based tool for building, visualizing and analyzing Adverse Outcome Pathway (AOP) networks. ![AOP-Suite logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/aopsuite.png) - -**Tool Webpage:** [https://aopsuite.cloud.vhp4safety.nl/](https://aopsuite.cloud.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [AOP Network Tool introduction](https://docs.vhp4safety.nl/en/latest/tutorials/aopsuite/aopsuite.html) +* Service Introduction: [AOP Network Tool introduction](https://docs.vhp4safety.nl/en/latest/tutorials/aopsuite/aopsuite.html) * Workflow: To be added @@ -42,15 +36,16 @@ A web-based tool for building, visualizing and analyzing Adverse Outcome Pathway } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://aopsuite.cloud.vhp4safety.nl/](https://aopsuite.cloud.vhp4safety.nl/) +* Development Cloud: [https://aopsuite.cloud.vhp4safety.nl/](https://aopsuite.cloud.vhp4safety.nl/) * Login Required: No @@ -102,6 +97,6 @@ A web-based tool for building, visualizing and analyzing Adverse Outcome Pathway "@id" : "https://vhp4safety.github.io/cloud/service/aopsuite", "name": "AOP-Suite", "description": "A web-based tool for building, visualizing and analyzing Adverse Outcome Pathway (AOP) networks.", - "url": "https://aopsuite.cloud.vhp4safety.nl/" + "url": "" } diff --git a/docs/service/aopwiki.md b/docs/service/aopwiki.md index e2ae7191..39d4aa73 100644 --- a/docs/service/aopwiki.md +++ b/docs/service/aopwiki.md @@ -1,23 +1,16 @@ - # AOP-Wiki Snorql UI - + A graphical interface for creating, preloading and exporting SPARQL queries tailored to your usecases. ![AOP-Wiki Snorql UI logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/aopwiki.png) -**Main Webpage:** [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) - -**Tool Webpage:** [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) - ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [AOP-Wiki SNORQL introduction](https://docs.vhp4safety.nl/en/latest/tutorials/aopwiki/aopwiki.html) -* Service Introduction: [AOP-Wiki SNORQL introduction](https://docs.vhp4safety.nl/en/latest/tutorials/aopwiki/aopwiki.html) - -* Workflow: [AOPLink: Extracting and Analyzing Data Related to an AOP of Interest](https://docs.vhp4safety.nl/en/latest/tutorials/aoplink/aoplink.html) +* Workflow: [AOPLink: Extracting and Analyzing Data Related to an AOP of Interest](https://docs.vhp4safety.nl/en/latest/tutorials/aoplink/aoplink.html) * Demo: To be added @@ -43,15 +36,16 @@ A graphical interface for creating, preloading and exporting SPARQL queries tail } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) +* Development Cloud: [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) * Login Required: No @@ -83,7 +77,7 @@ A graphical interface for creating, preloading and exporting SPARQL queries tail * Docker: [https://hub.docker.com/r/aammar/snorql-httpd](https://hub.docker.com/r/aammar/snorql-httpd) -* Bio.tools: [aop-wiki_rdf](https://bio.tools/aop-wiki_rdf) +* Bio.tools: [aop-wiki_rdf](aop-wiki_rdf) * FAIRsharing: Not available diff --git a/docs/service/aopwikiapi.md b/docs/service/aopwikiapi.md index 19cf0c2d..3c2f67d9 100644 --- a/docs/service/aopwikiapi.md +++ b/docs/service/aopwikiapi.md @@ -1,20 +1,13 @@ - # AOP-Wiki API - + A REST API for creating and accessing content in the AOP-Wiki database. ![AOP-Wiki API logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/aopwikiapi.png) -**Main Webpage:** [https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries](https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries) - -**Tool Webpage:** [https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries](https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries) - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -43,15 +36,16 @@ A REST API for creating and accessing content in the AOP-Wiki database. } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries](https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries) +* Development Cloud: [https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries](https://aopwiki-api.cloud.vhp4safety.nl/api/marvinm2/AOPWikiQueries) * Login Required: No diff --git a/docs/service/arrayanalysis.md b/docs/service/arrayanalysis.md index a774d663..4154bee9 100644 --- a/docs/service/arrayanalysis.md +++ b/docs/service/arrayanalysis.md @@ -1,21 +1,14 @@ - # ArrayAnalysis - + A user-interface for preprocessing and statistically analyzing RNA-sequencing and microarray transcriptomics data. ![ArrayAnalysis logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/arrayanalysis.png) -**Main Webpage:** [https://arrayanalysis.org/](https://arrayanalysis.org/) - -**Tool Webpage:** [https://arrayanalysis.vhp4safety.nl/](https://arrayanalysis.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [Microarray Analysis](https://arrayanalysis.org/details#Microarray_Analysis), [RNA-seq Analysis](https://arrayanalysis.org/details#RNA-seq_Analysis) +* Service Introduction: [Microarray Analysis;RNA-seq Analysis](https://arrayanalysis.org/details#Microarray_Analysis;https://arrayanalysis.org/details#RNA-seq_Analysis) * Workflow: To be added @@ -43,15 +36,16 @@ A user-interface for preprocessing and statistically analyzing RNA-sequencing an } } - + + ## VHP4Safety Service Metadata -* Stage: NA +* Stage: [NA](NA) -* Sub-Stage: NA +* Sub-stage: [NA](NA) -* Development Cloud: [https://arrayanalysis.vhp4safety.nl/](https://arrayanalysis.vhp4safety.nl/) +* Development Cloud: [https://arrayanalysis.vhp4safety.nl/](https://arrayanalysis.vhp4safety.nl/) * Login Required: Not available @@ -103,6 +97,6 @@ A user-interface for preprocessing and statistically analyzing RNA-sequencing an "@id" : "https://vhp4safety.github.io/cloud/service/arrayanalysis", "name": "ArrayAnalysis", "description": "A user-interface for preprocessing and statistically analyzing RNA-sequencing and microarray transcriptomics data.", - "url": "https://arrayanalysis.vhp4safety.nl/" + "url": "https://arrayanalysis.org/" } diff --git a/docs/service/biomodels.md b/docs/service/biomodels.md index bfe783f4..d58b1fa3 100644 --- a/docs/service/biomodels.md +++ b/docs/service/biomodels.md @@ -1,19 +1,13 @@ - # BioModels - + A repository dedicated to the inventory and acquisition of high-quality mathematical models pertaining to biological and biomedical systems. ![BioModels logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/biomodels.png) -**Main Webpage:** [https://www.ebi.ac.uk/biomodels/](https://www.ebi.ac.uk/biomodels/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ A repository dedicated to the inventory and acquisition of high-quality mathemat } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000055 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000055](https://vhp4safety.github.io/glossary#VHP0000055) * Development Cloud: Not available @@ -82,7 +77,7 @@ A repository dedicated to the inventory and acquisition of high-quality mathemat * Docker: Not available -* Bio.tools: [biomodels](https://bio.tools/biomodels) +* Bio.tools: [biomodels](biomodels) * FAIRsharing: Not available @@ -102,6 +97,6 @@ A repository dedicated to the inventory and acquisition of high-quality mathemat "@id" : "https://vhp4safety.github.io/cloud/service/biomodels", "name": "BioModels", "description": "A repository dedicated to the inventory and acquisition of high-quality mathematical models pertaining to biological and biomedical systems.", - "url": "" + "url": "https://www.ebi.ac.uk/biomodels/" } diff --git a/docs/service/biotransformer.md b/docs/service/biotransformer.md index ee09d75f..45c7f06f 100644 --- a/docs/service/biotransformer.md +++ b/docs/service/biotransformer.md @@ -1,19 +1,13 @@ - # BioTransformer - + A software tool for predicting metabolites from SMILES-formatted chemical inputs. ![BioTransformer logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/biotransformer.png) -**Main Webpage:** [https://biotransformer.ca/](https://biotransformer.ca/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ A software tool for predicting metabolites from SMILES-formatted chemical inputs } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) * Development Cloud: Not available @@ -60,7 +55,7 @@ A software tool for predicting metabolites from SMILES-formatted chemical inputs * Contact: Not available -* API Type: +* API Type: Not available * Categories: To be added @@ -82,7 +77,7 @@ A software tool for predicting metabolites from SMILES-formatted chemical inputs * Docker: Not available -* Bio.tools: [biotransformer](https://bio.tools/biotransformer) +* Bio.tools: [biotransformer](biotransformer) * FAIRsharing: Not available @@ -102,6 +97,6 @@ A software tool for predicting metabolites from SMILES-formatted chemical inputs "@id" : "https://vhp4safety.github.io/cloud/service/biotransformer", "name": "BioTransformer", "description": "A software tool for predicting metabolites from SMILES-formatted chemical inputs.", - "url": "" + "url": "https://biotransformer.ca/" } diff --git a/docs/service/bmdexpress_3.md b/docs/service/bmdexpress_3.md index cc089010..71690a1c 100644 --- a/docs/service/bmdexpress_3.md +++ b/docs/service/bmdexpress_3.md @@ -1,23 +1,18 @@ - # BMDExpress-3 - + A software tool for high-dimensional dose-response modeling and analysis. - -**Main Webpage:** [https://github.com/auerbachs/BMDExpress-3](https://github.com/auerbachs/BMDExpress-3) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation +* Service Introduction: []() -* Service Introduction: []() +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -41,25 +36,26 @@ A software tool for high-dimensional dose-response modeling and analysis. } } - + + ## VHP4Safety Service Metadata -* Stage: +* Stage: Not available -* Sub-Stage: +* Sub-stage: Not available * Development Cloud: Not available -* Login Required: +* Login Required: Not available -* TRL: +* TRL: Not available * Type: external * Contact: Scott Auerbach (auerbachs@niehs.nih.gov) -* API Type: +* API Type: Not available * Categories: To be added @@ -69,27 +65,27 @@ A software tool for high-dimensional dose-response modeling and analysis. ## Technical Tool Specifications -* Provider: []() +* Provider: Not available * Citation: [10.1186/1471-2164-8-387](https://doi.org/10.1186/1471-2164-8-387) * Version: 3.20.0106 -* License: +* License: Not available * Source Code: [https://github.com/auerbachs/BMDExpress-3](https://github.com/auerbachs/BMDExpress-3) -* Docker: []() +* Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/bridgedb.md b/docs/service/bridgedb.md index 14b28a23..f48307c8 100644 --- a/docs/service/bridgedb.md +++ b/docs/service/bridgedb.md @@ -1,23 +1,16 @@ - # BridgeDb - + A framework for mapping identifiers across biological databases and related sources. ![BridgeDb logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/bridgedb.png) -**Main Webpage:** [https://www.bridgedb.org/](https://www.bridgedb.org/) - -**Tool Webpage:** [https://bridgedb.cloud.vhp4safety.nl/](https://bridgedb.cloud.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [BridgeDb: Mapping Gene Identifiers](https://docs.vhp4safety.nl/en/latest/tutorials/bridgedb/gene_hgnc_name_to_ensembl.html) -* Service Introduction: [BridgeDb: Mapping Gene Identifiers](https://docs.vhp4safety.nl/en/latest/tutorials/bridgedb/gene_hgnc_name_to_ensembl.html) - -* Workflow: [Information about chemicals](https://docs.vhp4safety.nl/en/latest/tutorials/cheminfo/intro.html) +* Workflow: [Information about chemicals](https://docs.vhp4safety.nl/en/latest/tutorials/cheminfo/intro.html) * Demo: To be added @@ -43,15 +36,16 @@ A framework for mapping identifiers across biological databases and related sour } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000047 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000047](https://vhp4safety.github.io/glossary#VHP0000047) -* Development Cloud: [https://bridgedb.cloud.vhp4safety.nl/](https://bridgedb.cloud.vhp4safety.nl/) +* Development Cloud: [https://bridgedb.cloud.vhp4safety.nl/](https://bridgedb.cloud.vhp4safety.nl/) * Login Required: no @@ -59,7 +53,7 @@ A framework for mapping identifiers across biological databases and related sour * Type: internal -* Contact: Not available +* Contact: Egon Willighagen () * API Type: REST @@ -71,7 +65,7 @@ A framework for mapping identifiers across biological databases and related sour ## Technical Tool Specifications -* Provider: Not available +* Provider: [Department of Translational Genomics, Maastricht University]() * Citation: [10.1186/1471-2105-11-5](https://doi.org/10.1186/1471-2105-11-5) @@ -83,7 +77,7 @@ A framework for mapping identifiers across biological databases and related sour * Docker: [https://hub.docker.com/r/bigcatum/bridgedb](https://hub.docker.com/r/bigcatum/bridgedb) -* Bio.tools: [bridgedb](https://bio.tools/bridgedb) +* Bio.tools: [bridgedb](bridgedb) * FAIRsharing: [10.25504/FAIRsharing.5ry74y](10.25504/FAIRsharing.5ry74y) @@ -103,6 +97,6 @@ A framework for mapping identifiers across biological databases and related sour "@id" : "https://vhp4safety.github.io/cloud/service/bridgedb", "name": "BridgeDb", "description": "A framework for mapping identifiers across biological databases and related sources.", - "url": "https://bridgedb.cloud.vhp4safety.nl/" + "url": "https://www.bridgedb.org/" } diff --git a/docs/service/cdk.md b/docs/service/cdk.md index e263544a..3407e294 100644 --- a/docs/service/cdk.md +++ b/docs/service/cdk.md @@ -1,19 +1,14 @@ - # The Chemistry Development Kit - + A Java library for chem- and bioinformatics, with functionality to read/write chemical structures, calculate molecular descriptors, physicochemical properties, substructure and similarity searching, and much more. - -**Main Webpage:** [http://cdk.github.io/](http://cdk.github.io/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [Groovy Cheminformatics with the Chemistry Development Kit](https://cdk.github.io/cdkbook/) +* Service Introduction: [Groovy Cheminformatics with the Chemistry Development Kit](https://cdk.github.io/cdkbook/) * Workflow: To be added @@ -41,13 +36,14 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch } } - + + ## VHP4Safety Service Metadata -* Stage: Not available +* Stage: Not available -* Sub-Stage: Not available +* Sub-stage: Not available * Development Cloud: Not available @@ -81,7 +77,7 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch * Docker: Not available -* Bio.tools: [cdk](https://bio.tools/cdk) +* Bio.tools: [cdk](cdk) * FAIRsharing: Not available @@ -101,6 +97,6 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch "@id" : "https://vhp4safety.github.io/cloud/service/cdk", "name": "The Chemistry Development Kit", "description": "A Java library for chem- and bioinformatics, with functionality to read/write chemical structures, calculate molecular descriptors, physicochemical properties, substructure and similarity searching, and much more.", - "url": "" + "url": "http://cdk.github.io/" } diff --git a/docs/service/cdkdepict.md b/docs/service/cdkdepict.md index 0cf3cd1b..d9b2c7c6 100644 --- a/docs/service/cdkdepict.md +++ b/docs/service/cdkdepict.md @@ -1,20 +1,13 @@ - # CDK Depict - + A webservice for generating chemical structure images from SMILES inputs. ![CDK Depict logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/cdkdepict.png) -**Main Webpage:** [https://www.simolecule.com/cdkdepict/depict.html](https://www.simolecule.com/cdkdepict/depict.html) - -**Tool Webpage:** [https://cdkdepict.cloud.vhp4safety.nl/](https://cdkdepict.cloud.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -43,15 +36,16 @@ A webservice for generating chemical structure images from SMILES inputs. } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) -* Development Cloud: [https://cdkdepict.cloud.vhp4safety.nl/](https://cdkdepict.cloud.vhp4safety.nl/) +* Development Cloud: [https://cdkdepict.cloud.vhp4safety.nl/](https://cdkdepict.cloud.vhp4safety.nl/) * Login Required: no @@ -71,7 +65,7 @@ A webservice for generating chemical structure images from SMILES inputs. ## Technical Tool Specifications -* Provider: Not available +* Provider: [simolecule]() * Citation: [10.1186/s13321-017-0220-4](https://doi.org/10.1186/s13321-017-0220-4) @@ -83,7 +77,7 @@ A webservice for generating chemical structure images from SMILES inputs. * Docker: [https://hub.docker.com/r/simolecule/cdkdepict](https://hub.docker.com/r/simolecule/cdkdepict) -* Bio.tools: [cdk_depict](https://bio.tools/cdk_depict) +* Bio.tools: [cdk_depict](cdk_depict) * FAIRsharing: Not available @@ -103,6 +97,6 @@ A webservice for generating chemical structure images from SMILES inputs. "@id" : "https://vhp4safety.github.io/cloud/service/cdkdepict", "name": "CDK Depict", "description": "A webservice for generating chemical structure images from SMILES inputs.", - "url": "https://cdkdepict.cloud.vhp4safety.nl/" + "url": "https://www.simolecule.com/cdkdepict/depict.html" } diff --git a/docs/service/celldesigner.md b/docs/service/celldesigner.md index 0e762531..b75e6750 100644 --- a/docs/service/celldesigner.md +++ b/docs/service/celldesigner.md @@ -1,20 +1,14 @@ - # CellDesigner - + An intuitive user interface for creating gene-regulatory and biochemical network diagrams. ![CellDesigner logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/celldesigner.png) -**Main Webpage:** [https://www.celldesigner.org/](https://www.celldesigner.org/) - - ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [Quick Tutorial](https://www.celldesigner.org/help/CDH_QT.html) +* Service Introduction: [Quick Tutorial](https://www.celldesigner.org/help/CDH_QT.html) * Workflow: To be added @@ -42,13 +36,14 @@ An intuitive user interface for creating gene-regulatory and biochemical network } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: +* Sub-stage: Not available * Development Cloud: Not available @@ -102,6 +97,6 @@ An intuitive user interface for creating gene-regulatory and biochemical network "@id" : "https://vhp4safety.github.io/cloud/service/celldesigner", "name": "CellDesigner", "description": "An intuitive user interface for creating gene-regulatory and biochemical network diagrams.", - "url": "" + "url": "https://www.celldesigner.org/" } diff --git a/docs/service/comptox.md b/docs/service/comptox.md index b47dae1d..131360b8 100644 --- a/docs/service/comptox.md +++ b/docs/service/comptox.md @@ -1,19 +1,13 @@ - # CompTox - + An online database for searching chemical, toxicity and exposure information. ![CompTox logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/comptox.png) -**Main Webpage:** [https://comptox.epa.gov/dashboard/](https://comptox.epa.gov/dashboard/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An online database for searching chemical, toxicity and exposure information. } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) -* Sub-Stage: +* Sub-stage: Not available * Development Cloud: Not available @@ -102,6 +97,6 @@ An online database for searching chemical, toxicity and exposure information. "@id" : "https://vhp4safety.github.io/cloud/service/comptox", "name": "CompTox", "description": "An online database for searching chemical, toxicity and exposure information.", - "url": "" + "url": "https://comptox.epa.gov/dashboard/" } diff --git a/docs/service/copasi.md b/docs/service/copasi.md index 1305bf29..38248e8f 100644 --- a/docs/service/copasi.md +++ b/docs/service/copasi.md @@ -1,19 +1,13 @@ - # COPASI - + An open-source software for simulating, analyzing and visualizing biochemical networks using a wide range of methods. ![COPASI logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/copasi.png) -**Main Webpage:** [http://copasi.org/](http://copasi.org/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An open-source software for simulating, analyzing and visualizing biochemical ne } } - + + ## VHP4Safety Service Metadata -* Stage: Not available +* Stage: Not available -* Sub-Stage: Not available +* Sub-stage: Not available * Development Cloud: Not available @@ -82,7 +77,7 @@ An open-source software for simulating, analyzing and visualizing biochemical ne * Docker: Not available -* Bio.tools: [copasi](https://bio.tools/copasi) +* Bio.tools: [copasi](copasi) * FAIRsharing: Not available @@ -102,6 +97,6 @@ An open-source software for simulating, analyzing and visualizing biochemical ne "@id" : "https://vhp4safety.github.io/cloud/service/copasi", "name": "COPASI", "description": "An open-source software for simulating, analyzing and visualizing biochemical networks using a wide range of methods.", - "url": "" + "url": "http://copasi.org/" } diff --git a/docs/service/cplogd.md b/docs/service/cplogd.md index 9a22362a..b693afa5 100644 --- a/docs/service/cplogd.md +++ b/docs/service/cplogd.md @@ -1,20 +1,14 @@ - # cpLogD - + An online model for predicting water-octanol distribution coefficient (logD) of chemical compounds with confidence estimates. - -**Main Webpage:** [https://cplogd.cloud.vhp4safety.nl/](https://cplogd.cloud.vhp4safety.nl/) - -**Tool Webpage:** [https://cplogd.cloud.vhp4safety.nl/](https://cplogd.cloud.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [Predicting Water–Octanol Distribution Coefficient (logD) for Chemical Compounds](https://docs.vhp4safety.nl/en/latest/tutorials/cplogd/cplogd_tutorial.html) +* Service Introduction: [Predicting Water–Octanol Distribution Coefficient (logD) for Chemical Compounds](https://docs.vhp4safety.nl/en/latest/tutorials/cplogd/cplogd_tutorial.html) * Workflow: To be added @@ -42,15 +36,16 @@ An online model for predicting water-octanol distribution coefficient (logD) of } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) -* Development Cloud: [https://cplogd.cloud.vhp4safety.nl/](https://cplogd.cloud.vhp4safety.nl/) +* Development Cloud: [https://cplogd.cloud.vhp4safety.nl/](https://cplogd.cloud.vhp4safety.nl/) * Login Required: Not available diff --git a/docs/service/danish_qsar_database.md b/docs/service/danish_qsar_database.md index b847be96..54de99df 100644 --- a/docs/service/danish_qsar_database.md +++ b/docs/service/danish_qsar_database.md @@ -1,23 +1,18 @@ - # Danish (Q)SAR Database - + A freely available (Q)SAR tool for substance evaluations that includes estimates for from more than 200 (Q)SARs covering a wide range of hazardous properties relevant for human health and the environment. - -**Main Webpage:** [https://qsar.food.dtu.dk/](https://qsar.food.dtu.dk/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation +* Service Introduction: []() -* Service Introduction: []() +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -41,25 +36,26 @@ A freely available (Q)SAR tool for substance evaluations that includes estimates } } - + + ## VHP4Safety Service Metadata -* Stage: +* Stage: Not available -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: []() +* Development Cloud: Not available -* Login Required: +* Login Required: Not available -* TRL: +* TRL: Not available * Type: external * Contact: Technical University of Denmark (qsar@food.dtu.dk) -* API Type: +* API Type: Not available * Categories: To be added @@ -73,23 +69,23 @@ A freely available (Q)SAR tool for substance evaluations that includes estimates * Citation: [10.1016/j.toxlet.2016.06.1479](https://doi.org/10.1016/j.toxlet.2016.06.1479) -* Version: +* Version: Not available -* License: +* License: Not available -* Source Code: []() +* Source Code: Not available -* Docker: []() +* Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/decimer.md b/docs/service/decimer.md index 6e38e48e..24276db7 100644 --- a/docs/service/decimer.md +++ b/docs/service/decimer.md @@ -1,19 +1,13 @@ - # DECIMER - + An online service for automatically extracting chemical structure depictiions from PDFs and images. ![DECIMER logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/decimer.png) -**Main Webpage:** [https://decimer.ai/](https://decimer.ai/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,25 +36,26 @@ An online service for automatically extracting chemical structure depictiions fr } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) * Development Cloud: Not available * Login Required: No -* TRL: +* TRL: Not available * Type: external * Contact: Kohulan Rajan (kohulan.rajan@uni-jena.de) -* API Type: +* API Type: Not available * Categories: To be added @@ -82,11 +77,11 @@ An online service for automatically extracting chemical structure depictiions fr * Docker: [https://github.com/OBrink/DECIMER_Web](https://github.com/OBrink/DECIMER_Web) -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available * FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available * RSD: Not available @@ -102,6 +97,6 @@ An online service for automatically extracting chemical structure depictiions fr "@id" : "https://vhp4safety.github.io/cloud/service/decimer", "name": "DECIMER", "description": "An online service for automatically extracting chemical structure depictiions from PDFs and images.", - "url": "" + "url": "https://decimer.ai/" } diff --git a/docs/service/dsld.md b/docs/service/dsld.md index ead1b22d..0c144c74 100644 --- a/docs/service/dsld.md +++ b/docs/service/dsld.md @@ -1,18 +1,13 @@ - # NIH Dietary Supplement Label Database - + An online database from the NIH Office of Dietary Supplements that lets you explore information from more than 200,000 dietary supplement labels sold in the United States. - -**Main Webpage:** [https://dsld.od.nih.gov/](https://dsld.od.nih.gov/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ An online database from the NIH Office of Dietary Supplements that lets you expl } } - + + ## VHP4Safety Service Metadata -* Stage: external exposure +* Stage: [external exposure](external exposure) -* Sub-Stage: compound characteristics +* Sub-stage: [compound characteristics](compound characteristics) * Development Cloud: Not available @@ -101,6 +97,6 @@ An online database from the NIH Office of Dietary Supplements that lets you expl "@id" : "https://vhp4safety.github.io/cloud/service/dsld", "name": "NIH Dietary Supplement Label Database", "description": "An online database from the NIH Office of Dietary Supplements that lets you explore information from more than 200,000 dietary supplement labels sold in the United States.", - "url": "" + "url": "https://dsld.od.nih.gov/" } diff --git a/docs/service/ema_documents.md b/docs/service/ema_documents.md index 0b38814a..db122a09 100644 --- a/docs/service/ema_documents.md +++ b/docs/service/ema_documents.md @@ -1,19 +1,13 @@ - # European Medicines Agency Documents - + An online repository for inventarisation of official reports from the European Medicines Agency concerning chemical evaluation and safety monitoring. ![European Medicines Agency Documents logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/ema_documents.png) -**Main Webpage:** [https://www.ema.europa.eu/en/search](https://www.ema.europa.eu/en/search) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An online repository for inventarisation of official reports from the European M } } - + + ## VHP4Safety Service Metadata -* Stage: external exposure +* Stage: [external exposure](external exposure) -* Sub-Stage: compound characteristics +* Sub-stage: [compound characteristics](compound characteristics) * Development Cloud: Not available @@ -102,6 +97,6 @@ An online repository for inventarisation of official reports from the European M "@id" : "https://vhp4safety.github.io/cloud/service/ema_documents", "name": "European Medicines Agency Documents", "description": "An online repository for inventarisation of official reports from the European Medicines Agency concerning chemical evaluation and safety monitoring.", - "url": "" + "url": "https://www.ema.europa.eu/en/search" } diff --git a/docs/service/endocrine_disruptome.md b/docs/service/endocrine_disruptome.md index fa0845e8..118fc5cd 100644 --- a/docs/service/endocrine_disruptome.md +++ b/docs/service/endocrine_disruptome.md @@ -1,23 +1,18 @@ - # Endocrine Disruptome - + An open source, user friendly and web based prediction tool that uses molecular docking to predict binding of compounds to 14 different nuclear receptors. - -**Main Webpage:** [http://endocrinedisruptome.ki.si/](http://endocrinedisruptome.ki.si/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [Tool's Frequently Asked Questions](http://endocrinedisruptome.ki.si/FAQ.html) -* Service Introduction: [Tool's Frequently Asked Questions](http://endocrinedisruptome.ki.si/FAQ.html) +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -41,25 +36,26 @@ An open source, user friendly and web based prediction tool that uses molecular } } - + + ## VHP4Safety Service Metadata -* Stage: +* Stage: Not available -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: []() +* Development Cloud: Not available -* Login Required: +* Login Required: Not available -* TRL: +* TRL: Not available * Type: external * Contact: Katra Kolšek (katra.kolsek@ffa.uni-lj.si) -* API Type: +* API Type: Not available * Categories: To be added @@ -73,23 +69,23 @@ An open source, user friendly and web based prediction tool that uses molecular * Citation: [10.1021/ci400649p](https://doi.org/10.1021/ci400649p) -* Version: +* Version: Not available * License: BSD-3-Clause license * Source Code: [https://github.com/katrakolsek/DoTS](https://github.com/katrakolsek/DoTS) -* Docker: []() +* Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/fairdomhub.md b/docs/service/fairdomhub.md index 63cd3698..da624c6c 100644 --- a/docs/service/fairdomhub.md +++ b/docs/service/fairdomhub.md @@ -1,19 +1,13 @@ - # FAIRDOMHub - + A web-accessible registry for managing, sharing and organising research data and research assets. ![FAIRDOMHub logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/fairdomhub.png) -**Main Webpage:** [https://fairdomhub.org/](https://fairdomhub.org/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ A web-accessible registry for managing, sharing and organising research data and } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: +* Sub-stage: Not available * Development Cloud: Not available @@ -102,6 +97,6 @@ A web-accessible registry for managing, sharing and organising research data and "@id" : "https://vhp4safety.github.io/cloud/service/fairdomhub", "name": "FAIRDOMHub", "description": "A web-accessible registry for managing, sharing and organising research data and research assets.", - "url": "" + "url": "https://fairdomhub.org/" } diff --git a/docs/service/fairspace.md b/docs/service/fairspace.md index 4c5b5592..1ff625cf 100644 --- a/docs/service/fairspace.md +++ b/docs/service/fairspace.md @@ -1,19 +1,13 @@ - # Fairspace - + An open source RDF-based data management platform for importing and exporting research-relevant metadata ![Fairspace logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/fairspace.png) -**Main Webpage:** [https://www.thehyve.nl/services/fairspace](https://www.thehyve.nl/services/fairspace) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An open source RDF-based data management platform for importing and exporting re } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000049 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000049](https://vhp4safety.github.io/glossary#VHP0000049) * Development Cloud: Not available @@ -102,6 +97,6 @@ An open source RDF-based data management platform for importing and exporting re "@id" : "https://vhp4safety.github.io/cloud/service/fairspace", "name": "Fairspace", "description": "An open source RDF-based data management platform for importing and exporting research-relevant metadata", - "url": "" + "url": "https://www.thehyve.nl/services/fairspace" } diff --git a/docs/service/farmacokompas.md b/docs/service/farmacokompas.md index afefbcf5..7cf33a9b 100644 --- a/docs/service/farmacokompas.md +++ b/docs/service/farmacokompas.md @@ -1,19 +1,13 @@ - # Farmacotherapeutisch Kompas - + A Dutch online resource for gathering data on the pharmacology, adverse effects, and prices of all pharmaceutical products available in the Netherlands. ![Farmacotherapeutisch Kompas logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/farmacokompas.png) -**Main Webpage:** [https://www.farmacotherapeutischkompas.nl/](https://www.farmacotherapeutischkompas.nl/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ A Dutch online resource for gathering data on the pharmacology, adverse effects, } } - + + ## VHP4Safety Service Metadata -* Stage: external exposure +* Stage: [external exposure](external exposure) -* Sub-Stage: compound characteristics +* Sub-stage: [compound characteristics](compound characteristics) * Development Cloud: Not available @@ -102,6 +97,6 @@ A Dutch online resource for gathering data on the pharmacology, adverse effects, "@id" : "https://vhp4safety.github.io/cloud/service/farmacokompas", "name": "Farmacotherapeutisch Kompas", "description": "A Dutch online resource for gathering data on the pharmacology, adverse effects, and prices of all pharmaceutical products available in the Netherlands.", - "url": "" + "url": "https://www.farmacotherapeutischkompas.nl/" } diff --git a/docs/service/flame.md b/docs/service/flame.md index a56174f6..9742fd29 100644 --- a/docs/service/flame.md +++ b/docs/service/flame.md @@ -1,19 +1,13 @@ - # Flame - + An open source web application for building predictive models from biologically annotated chemical structures using predefined workflows. - -**Main Webpage:** [https://phi.upf.edu/phi/index.php/software/flame/](https://phi.upf.edu/phi/index.php/software/flame/) - -**Tool Webpage:** [http://flame.cloud.vhp4safety.nl:8098/](http://flame.cloud.vhp4safety.nl:8098/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,15 +36,16 @@ An open source web application for building predictive models from biologically } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: [http://flame.cloud.vhp4safety.nl:8098/](http://flame.cloud.vhp4safety.nl:8098/) +* Development Cloud: [http://flame.cloud.vhp4safety.nl:8098/](http://flame.cloud.vhp4safety.nl:8098/) * Login Required: Not available @@ -102,6 +97,6 @@ An open source web application for building predictive models from biologically "@id" : "https://vhp4safety.github.io/cloud/service/flame", "name": "Flame", "description": "An open source web application for building predictive models from biologically annotated chemical structures using predefined workflows.", - "url": "http://flame.cloud.vhp4safety.nl:8098/" + "url": "https://phi.upf.edu/phi/index.php/software/flame/" } diff --git a/docs/service/google.md b/docs/service/google.md index 4b007a9b..98a69720 100644 --- a/docs/service/google.md +++ b/docs/service/google.md @@ -1,18 +1,13 @@ - # Google Search - + Online search engine for Google. - -**Main Webpage:** [https://google.com/](https://google.com/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ Online search engine for Google. } } - + + ## VHP4Safety Service Metadata -* Stage: generic +* Stage: [generic](generic) -* Sub-Stage: mechanisms of toxicity / compound characteristics +* Sub-stage: [mechanisms of toxicity / compound characteristics](mechanisms of toxicity / compound characteristics) * Development Cloud: Not available @@ -101,6 +97,6 @@ Online search engine for Google. "@id" : "https://vhp4safety.github.io/cloud/service/google", "name": "Google Search", "description": "Online search engine for Google.", - "url": "" + "url": "https://google.com/" } diff --git a/docs/service/gscholar.md b/docs/service/gscholar.md index a54c9f19..d6f7ee4e 100644 --- a/docs/service/gscholar.md +++ b/docs/service/gscholar.md @@ -1,18 +1,13 @@ - # Google Scholar - + An online search engine for (scientific) literature. - -**Main Webpage:** [https://scholar.google.com/](https://scholar.google.com/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ An online search engine for (scientific) literature. } } - + + ## VHP4Safety Service Metadata -* Stage: generic +* Stage: [generic](generic) -* Sub-Stage: mechanisms of toxicity / compound characteristics +* Sub-stage: [mechanisms of toxicity / compound characteristics](mechanisms of toxicity / compound characteristics) * Development Cloud: Not available @@ -101,6 +97,6 @@ An online search engine for (scientific) literature. "@id" : "https://vhp4safety.github.io/cloud/service/gscholar", "name": "Google Scholar", "description": "An online search engine for (scientific) literature.", - "url": "" + "url": "https://scholar.google.com/" } diff --git a/docs/service/jrc_data_catalogue.md b/docs/service/jrc_data_catalogue.md index 8ead4941..007010f9 100644 --- a/docs/service/jrc_data_catalogue.md +++ b/docs/service/jrc_data_catalogue.md @@ -1,19 +1,13 @@ - # Joint Research Centre Data Catalogue - + An in-house data inventory produced by the Joint Research Centre (JRC) for provision of independent scientific advice and support to policies of the European Union. ![Joint Research Centre Data Catalogue logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/jrc_data_catalogue.png) -**Main Webpage:** [https://data.jrc.ec.europa.eu/](https://data.jrc.ec.europa.eu/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An in-house data inventory produced by the Joint Research Centre (JRC) for provi } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000049 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000049](https://vhp4safety.github.io/glossary#VHP0000049) * Development Cloud: Not available @@ -102,6 +97,6 @@ An in-house data inventory produced by the Joint Research Centre (JRC) for provi "@id" : "https://vhp4safety.github.io/cloud/service/jrc_data_catalogue", "name": "Joint Research Centre Data Catalogue", "description": "An in-house data inventory produced by the Joint Research Centre (JRC) for provision of independent scientific advice and support to policies of the European Union.", - "url": "" + "url": "https://data.jrc.ec.europa.eu/" } diff --git a/docs/service/llemy.md b/docs/service/llemy.md index dca92e80..ddaa933a 100644 --- a/docs/service/llemy.md +++ b/docs/service/llemy.md @@ -1,23 +1,18 @@ - # Llemy - + An online tool for answering questions about lipid metabolism and related toxicology/biology using MINERVA pathway knowledge, live web research and AI-generated summaries. - - -**Tool Webpage:** [https://llemy.vhp4safety.nl/](https://llemy.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added -* Demo: [Hosted pilot](https://llemy.vhp4safety.nl/) +* Demo: [Hosted pilot](https://llemy.vhp4safety.nl/)

@@ -41,15 +36,16 @@ An online tool for answering questions about lipid metabolism and related toxico } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: prototype +* Sub-stage: [prototype](prototype) -* Development Cloud: [https://llemy.vhp4safety.nl/](https://llemy.vhp4safety.nl/) +* Development Cloud: [https://llemy.vhp4safety.nl/](https://llemy.vhp4safety.nl/) * Login Required: Not available @@ -81,15 +77,15 @@ An online tool for answering questions about lipid metabolism and related toxico * Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/mct8-dock.md b/docs/service/mct8-dock.md index e7314b21..b9e88dd7 100644 --- a/docs/service/mct8-dock.md +++ b/docs/service/mct8-dock.md @@ -1,19 +1,14 @@ - # MCT8 Docking for MIE Discovery - + A Python-based notebook for identifying potential MCT8 inhibitors and related molecular events linked to developmental thyroid toxicity from maternal thyroid hormone deprivation. - -**Main Webpage:** [https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [SOM Prediction: Site-of-Metabolism Prediction](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) +* Service Introduction: [SOM Prediction: Site-of-Metabolism Prediction](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) * Workflow: To be added @@ -41,19 +36,20 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo } } - + + ## VHP4Safety Service Metadata -* Stage: +* Stage: Not available -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: []() +* Development Cloud: Not available * Login Required: No -* TRL: +* TRL: Not available * Type: External @@ -69,9 +65,9 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo ## Technical Tool Specifications -* Provider: Not available +* Provider: [David Poole]() -* Citation: [](https://doi.org/) +* Citation: Not available * Version: Not available @@ -85,7 +81,7 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo * FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available * RSD: Not available @@ -101,6 +97,6 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo "@id" : "https://vhp4safety.github.io/cloud/service/mct8-dock", "name": "MCT8 Docking for MIE Discovery", "description": "A Python-based notebook for identifying potential MCT8 inhibitors and related molecular events linked to developmental thyroid toxicity from maternal thyroid hormone deprivation.", - "url": "" + "url": "https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing" } diff --git a/docs/service/molaopanalyser.md b/docs/service/molaopanalyser.md index 30f39cea..9a6a6072 100644 --- a/docs/service/molaopanalyser.md +++ b/docs/service/molaopanalyser.md @@ -1,24 +1,18 @@ - # MolAOP analyser - + An online service for analyzing transcriptomic data in the context of molecular Adverse Outcome Pathways (AOPs), supporting data upload or demo datasets for gene selection, visualization and Key Event (KE) enrichment analysis. - -**Main Webpage:** [https://molaop-analyser.vhp4safety.nl/](https://molaop-analyser.vhp4safety.nl/) - -**Tool Webpage:** [https://molaop-analyser.vhp4safety.nl/](https://molaop-analyser.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [Molecular Adverse Outcome Pathway analyser tutorial](https://docs.vhp4safety.nl/en/latest/tutorials/molaopanalyser/molaopanalyser.html) -* Service Introduction: [Molecular Adverse Outcome Pathway analyser tutorial](https://docs.vhp4safety.nl/en/latest/tutorials/molaopanalyser/molaopanalyser.html) +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -42,25 +36,26 @@ An online service for analyzing transcriptomic data in the context of molecular } } - + + ## VHP4Safety Service Metadata -* Stage: +* Stage: Not available -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: [https://molaop-analyser.vhp4safety.nl/](https://molaop-analyser.vhp4safety.nl/) +* Development Cloud: [https://molaop-analyser.vhp4safety.nl/](https://molaop-analyser.vhp4safety.nl/) -* Login Required: +* Login Required: Not available -* TRL: +* TRL: Not available * Type: internal * Contact: Marvin Martens (marvin.martens@maastrichtuniversity.nl) -* API Type: +* API Type: Not available * Categories: To be added @@ -72,25 +67,25 @@ An online service for analyzing transcriptomic data in the context of molecular * Provider: [Maastricht University](maastrichtuniversity.nl) -* Citation: [](https://doi.org/) +* Citation: Not available -* Version: +* Version: Not available -* License: +* License: Not available * Source Code: [https://github.com/marvinm2/molAOP-analyser](https://github.com/marvinm2/molAOP-analyser) -* Docker: []() +* Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000056 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000056](https://vhp4safety.github.io/glossary#VHP0000056) -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: []() +* Development Cloud: Not available * Login Required: Not available -* TRL: +* TRL: Not available * Type: external @@ -78,9 +73,9 @@ A software for supporting chemical hazard assessment and enhancing mechanistic k * License: [Terms of Conditions](https://www.oecd.org/termsandconditions/) -* Source Code: []() +* Source Code: Not available -* Docker: []() +* Docker: Not available * Bio.tools: Not available @@ -102,6 +97,6 @@ A software for supporting chemical hazard assessment and enhancing mechanistic k "@id" : "https://vhp4safety.github.io/cloud/service/oecd_qsar_toolbox", "name": "The OECD QSAR Toolbox", "description": "A software for supporting chemical hazard assessment and enhancing mechanistic knowledge of substances in a cost-effective way.", - "url": "" + "url": "https://qsartoolbox.org/" } diff --git a/docs/service/ontox_physiological_maps.md b/docs/service/ontox_physiological_maps.md index 00202235..9c0ac7d5 100644 --- a/docs/service/ontox_physiological_maps.md +++ b/docs/service/ontox_physiological_maps.md @@ -1,18 +1,13 @@ - # ONTOX Physiological Maps - + Maps for illustrating biological processes behind toxicological risks using a standardized graphical notation. - -**Main Webpage:** [https://sites.google.com/view/ontox-maps/home](https://sites.google.com/view/ontox-maps/home) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ Maps for illustrating biological processes behind toxicological risks using a st } } - + + ## VHP4Safety Service Metadata -* Stage: Not available +* Stage: Not available -* Sub-Stage: Not available +* Sub-stage: Not available * Development Cloud: Not available @@ -69,7 +65,7 @@ Maps for illustrating biological processes behind toxicological risks using a st ## Technical Tool Specifications -* Provider: Not available +* Provider: [ONTOX]() * Citation: [10.14573/altex.2412241](https://doi.org/10.14573/altex.2412241) @@ -101,6 +97,6 @@ Maps for illustrating biological processes behind toxicological risks using a st "@id" : "https://vhp4safety.github.io/cloud/service/ontox_physiological_maps", "name": "ONTOX Physiological Maps", "description": "Maps for illustrating biological processes behind toxicological risks using a standardized graphical notation.", - "url": "" + "url": "https://sites.google.com/view/ontox-maps/home" } diff --git a/docs/service/oppbk_model.md b/docs/service/oppbk_model.md index 33f292a5..5fd77256 100644 --- a/docs/service/oppbk_model.md +++ b/docs/service/oppbk_model.md @@ -1,20 +1,13 @@ - # OP PBK Model - + An online physiologically based pharmacokinetic model for organophosphates ![OP PBK Model logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/oppbk_model.png) -**Main Webpage:** [http://oppbk.cloud.vhp4safety.nl/](http://oppbk.cloud.vhp4safety.nl/) - -**Tool Webpage:** [http://oppbk.cloud.vhp4safety.nl/](http://oppbk.cloud.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -43,15 +36,16 @@ An online physiologically based pharmacokinetic model for organophosphates } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000056 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000056](https://vhp4safety.github.io/glossary#VHP0000056) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000061 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000061](https://vhp4safety.github.io/glossary#VHP0000061) -* Development Cloud: [http://oppbk.cloud.vhp4safety.nl/](http://oppbk.cloud.vhp4safety.nl/) +* Development Cloud: [http://oppbk.cloud.vhp4safety.nl/](http://oppbk.cloud.vhp4safety.nl/) * Login Required: Not available diff --git a/docs/service/opsin.md b/docs/service/opsin.md index a1a2fc2a..fbb02d4b 100644 --- a/docs/service/opsin.md +++ b/docs/service/opsin.md @@ -1,19 +1,13 @@ - # OPSIN: Open Parser for Systematic IUPAC nomenclature - + An online service for parsing chemical IUPAC names into a machine-readable chemical identifiers. ![OPSIN: Open Parser for Systematic IUPAC nomenclature logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/opsin.png) -**Main Webpage:** [https://www.ebi.ac.uk/opsin/](https://www.ebi.ac.uk/opsin/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,13 +36,14 @@ An online service for parsing chemical IUPAC names into a machine-readable chemi } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) * Development Cloud: Not available @@ -58,9 +53,9 @@ An online service for parsing chemical IUPAC names into a machine-readable chemi * Type: Not available -* Contact: Not available +* Contact: Daniel Lowe () -* API Type: +* API Type: Not available * Categories: To be added @@ -102,6 +97,6 @@ An online service for parsing chemical IUPAC names into a machine-readable chemi "@id" : "https://vhp4safety.github.io/cloud/service/opsin", "name": "OPSIN: Open Parser for Systematic IUPAC nomenclature", "description": "An online service for parsing chemical IUPAC names into a machine-readable chemical identifiers.", - "url": "" + "url": "https://www.ebi.ac.uk/opsin/" } diff --git a/docs/service/oqt_assistant.md b/docs/service/oqt_assistant.md index c47f19c1..fe7c4d7f 100644 --- a/docs/service/oqt_assistant.md +++ b/docs/service/oqt_assistant.md @@ -1,25 +1,18 @@ - # O-QT — OECD QSAR Toolbox AI Assistant - + An online assistant for using the OECD QSAR Toolbox to analyze chemicals, assess hazards and generate AI-based summary reports. ![O-QT — OECD QSAR Toolbox AI Assistant logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/oqt_assistant.png) -**Main Webpage:** [https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant) - -**Tool Webpage:** [https://o-qt-oecd.vhp4safety.nl/](https://o-qt-oecd.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [O’QT README (single source of truth);FAQ](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md;https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md#faq) -* Service Introduction: [O’QT README (single source of truth)](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md), [FAQ](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md#faq) +* Workflow: [Agent Workflow (Context → Specialists → Read-Across → Synthesis)](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md#qsar-assistant-workflow) -* Workflow: [Agent Workflow (Context → Specialists → Read-Across → Synthesis)](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/README.md#qsar-assistant-workflow) - -* Demo: []() +* Demo: []()

@@ -43,15 +36,16 @@ An online assistant for using the OECD QSAR Toolbox to analyze chemicals, assess } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: prototype +* Sub-stage: [prototype](prototype) -* Development Cloud: [https://o-qt-oecd.vhp4safety.nl/](https://o-qt-oecd.vhp4safety.nl/) +* Development Cloud: [https://o-qt-oecd.vhp4safety.nl/](https://o-qt-oecd.vhp4safety.nl/) * Login Required: Requires a locally installed OECD QSAR Toolbox with Web API enabled on Windows; set QSAR_TOOLBOX_API_URL. Provide an OpenAI API key for AI analysis. @@ -61,7 +55,7 @@ An online assistant for using the OECD QSAR Toolbox to analyze chemicals, assess * Contact: Ivo Djidrovski (i.djidrovski@uu.nl) -* API Type: +* API Type: Not available * Categories: To be added @@ -83,15 +77,15 @@ An online assistant for using the OECD QSAR Toolbox to analyze chemicals, assess * Docker: [https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/Dockerfile](https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant/blob/main/Dockerfile) -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available * TeSS: [O-QT Assistant](O-QT Assistant) -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/qaop_app.md b/docs/service/qaop_app.md index b31d5947..945630c4 100644 --- a/docs/service/qaop_app.md +++ b/docs/service/qaop_app.md @@ -1,20 +1,14 @@ - # qAOP-App - + An interactive tool for visualizing and predicting key events (KEs) and adverse outcomes (AOs) over time using ODE-based qAOP models, illustrated with VHP4Safety case studies. - -**Main Webpage:** [https://qaop.vhp4safety.nl/](https://qaop.vhp4safety.nl/) - -**Tool Webpage:** [https://qaop.vhp4safety.nl/](https://qaop.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [qAOP App: Predicting Key Events and Adverse Outcomes Over Time](https://docs.vhp4safety.nl/en/latest/tutorials/qaop_app/qaop_tutorial.html) +* Service Introduction: [qAOP App: Predicting Key Events and Adverse Outcomes Over Time](https://docs.vhp4safety.nl/en/latest/tutorials/qaop_app/qaop_tutorial.html) * Workflow: To be added @@ -42,15 +36,16 @@ An interactive tool for visualizing and predicting key events (KEs) and adverse } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://qaop.vhp4safety.nl/](https://qaop.vhp4safety.nl/) +* Development Cloud: [https://qaop.vhp4safety.nl/](https://qaop.vhp4safety.nl/) * Login Required: Not available diff --git a/docs/service/qsprpred.md b/docs/service/qsprpred.md index 9c79edee..3f95d751 100644 --- a/docs/service/qsprpred.md +++ b/docs/service/qsprpred.md @@ -1,21 +1,14 @@ - # QSPRpred - + An online tool for chemical activity prediction for various endpoints using target-specific and pretrained QSAR models. ![QSPRpred logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/qsprpred.png) -**Main Webpage:** [https://qsprpred.cloud.vhp4safety.nl/](https://qsprpred.cloud.vhp4safety.nl/) - -**Tool Webpage:** [https://qsprpred.cloud.vhp4safety.nl/](https://qsprpred.cloud.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [QSPRpred App: Predicting Molecular Initiating Event Activation based on chemical structure](https://github.com/VHP4Safety/vhp4safety-docs/blob/main/tutorials/qsprpred_app/qsprpred_tutorial.md) +* Service Introduction: [QSPRpred App: Predicting Molecular Initiating Event Activation based on chemical structure](https://github.com/VHP4Safety/vhp4safety-docs/blob/main/tutorials/qsprpred_app/qsprpred_tutorial.md) * Workflow: To be added @@ -43,15 +36,16 @@ An online tool for chemical activity prediction for various endpoints using targ } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: [https://qsprpred.cloud.vhp4safety.nl/](https://qsprpred.cloud.vhp4safety.nl/) +* Development Cloud: [https://qsprpred.cloud.vhp4safety.nl/](https://qsprpred.cloud.vhp4safety.nl/) * Login Required: No @@ -61,7 +55,7 @@ An online tool for chemical activity prediction for various endpoints using targ * Contact: Linde Schoenmaker (l.schoenmaker@lacdr.leidenuniv.nl) -* API Type: +* API Type: Not available * Categories: To be added @@ -71,7 +65,7 @@ An online tool for chemical activity prediction for various endpoints using targ ## Technical Tool Specifications -* Provider: Not available +* Provider: [Department of Medicinal Chemistry,Leiden University]() * Citation: [10.26434/chemrxiv-2025-jr9v7](https://doi.org/10.26434/chemrxiv-2025-jr9v7) diff --git a/docs/service/r_odaf.md b/docs/service/r_odaf.md index 5070bdf2..c83cc9be 100644 --- a/docs/service/r_odaf.md +++ b/docs/service/r_odaf.md @@ -1,23 +1,18 @@ - # R-ODAF Shiny - + An R Shiny interface for the R-ODAF framework that provides standardised RNA-seq differential expression analysis for regulatory toxicology applications. - - -**Tool Webpage:** [https://r-odaf.nl/](https://r-odaf.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation +* Service Introduction: []() -* Service Introduction: []() +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -41,25 +36,26 @@ An R Shiny interface for the R-ODAF framework that provides standardised RNA-seq } } - + + ## VHP4Safety Service Metadata -* Stage: Toxicodynamics/AOP +* Stage: [Toxicodynamics/AOP](Toxicodynamics/AOP) -* Sub-Stage: Transcriptomics / Differential Expression +* Sub-stage: [Transcriptomics / Differential Expression](Transcriptomics / Differential Expression) -* Development Cloud: [https://r-odaf.nl/](https://r-odaf.nl/) +* Development Cloud: [https://r-odaf.nl/](https://r-odaf.nl/) -* Login Required: +* Login Required: Not available -* TRL: +* TRL: Not available * Type: internal * Contact: Saad Lodhi (saad.lodhi@maastrichtuniversity.nl) -* API Type: +* API Type: Not available * Categories: To be added @@ -73,23 +69,23 @@ An R Shiny interface for the R-ODAF framework that provides standardised RNA-seq * Citation: Not available -* Version: +* Version: Not available * License: MIT * Source Code: [https://github.com/fcaiment/R-ODAF/tree/shiny-version](https://github.com/fcaiment/R-ODAF/tree/shiny-version) -* Docker: []() +* Docker: Not available -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available * TeSS: [R-ODAF](R-ODAF) -* RSD: []() +* RSD: Not available -* Wikipedia: []() +* Wikipedia: Not available diff --git a/docs/service/sombie.md b/docs/service/sombie.md index e1be254a..fbd91296 100644 --- a/docs/service/sombie.md +++ b/docs/service/sombie.md @@ -1,20 +1,14 @@ - # SOM Prediction - + A webservice for prediction of protein-structure and reactivity based (P450) site-of-metabolism. - -**Main Webpage:** [https://sombie.cloud.vhp4safety.nl/](https://sombie.cloud.vhp4safety.nl/) - -**Tool Webpage:** [https://sombie.cloud.vhp4safety.nl/](https://sombie.cloud.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - -* Service Introduction: [SOM Prediction: Site-of-Metabolism Prediction](https://docs.vhp4safety.nl/en/latest/tutorials/sombie/site_of_metabolism_prediction.html) +* Service Introduction: [SOM Prediction: Site-of-Metabolism Prediction](https://docs.vhp4safety.nl/en/latest/tutorials/sombie/site_of_metabolism_prediction.html) * Workflow: To be added @@ -42,15 +36,16 @@ A webservice for prediction of protein-structure and reactivity based (P450) sit } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000056 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000056](https://vhp4safety.github.io/glossary#VHP0000056) -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: [https://sombie.cloud.vhp4safety.nl/](https://sombie.cloud.vhp4safety.nl/) +* Development Cloud: [https://sombie.cloud.vhp4safety.nl/](https://sombie.cloud.vhp4safety.nl/) * Login Required: No diff --git a/docs/service/sysrev.md b/docs/service/sysrev.md index 6a08604f..a8bec1e9 100644 --- a/docs/service/sysrev.md +++ b/docs/service/sysrev.md @@ -1,18 +1,13 @@ - # SysRev - + An online service for conduction of literature review, data extraction and systematic review. - -**Main Webpage:** [https://sysrev.com/](https://sysrev.com/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ An online service for conduction of literature review, data extraction and syste } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000053 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000053](https://vhp4safety.github.io/glossary#VHP0000053) * Development Cloud: Not available @@ -81,7 +77,7 @@ An online service for conduction of literature review, data extraction and syste * Docker: Not available -* Bio.tools: [sysrev](https://bio.tools/sysrev) +* Bio.tools: [sysrev](sysrev) * FAIRsharing: Not available @@ -101,6 +97,6 @@ An online service for conduction of literature review, data extraction and syste "@id" : "https://vhp4safety.github.io/cloud/service/sysrev", "name": "SysRev", "description": "An online service for conduction of literature review, data extraction and systematic review.", - "url": "" + "url": "https://sysrev.com/" } diff --git a/docs/service/toxtemp_assistant.md b/docs/service/toxtemp_assistant.md index 7a5ce676..cefa429a 100644 --- a/docs/service/toxtemp_assistant.md +++ b/docs/service/toxtemp_assistant.md @@ -1,25 +1,18 @@ - # ToxTempAssistant - + An online tool for harmonizing in vitro toxicity test methods using Large Language Models, based on the ToxTemp template where it extracts details from protocols, publications or lab notes to create structured draft responses. ![ToxTempAssistant logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/toxtemp_assistant.png) -**Main Webpage:** [https://toxtempassistant.vhp4safety.nl/](https://toxtempassistant.vhp4safety.nl/) - -**Tool Webpage:** [https://toxtempassistant.vhp4safety.nl/](https://toxtempassistant.vhp4safety.nl/) - ## Documentation -#### VHP4Safety Documentation +* Service Introduction: []() -* Service Introduction: []() +* Workflow: []() -* Workflow: []() - -* Demo: []() +* Demo: []()

@@ -43,17 +36,18 @@ An online tool for harmonizing in vitro toxicity test methods using Large Langua } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: +* Sub-stage: Not available -* Development Cloud: [https://toxtempassistant.vhp4safety.nl/](https://toxtempassistant.vhp4safety.nl/) +* Development Cloud: [https://toxtempassistant.vhp4safety.nl/](https://toxtempassistant.vhp4safety.nl/) -* Login Required: +* Login Required: Not available * TRL: TRL6 @@ -61,7 +55,7 @@ An online tool for harmonizing in vitro toxicity test methods using Large Langua * Contact: Jente Houweling (jente.houweling@rivm.nl) -* API Type: +* API Type: Not available * Categories: To be added @@ -83,15 +77,15 @@ An online tool for harmonizing in vitro toxicity test methods using Large Langua * Docker: [https://github.com/johannehouweling/ToxTempAssistant](https://github.com/johannehouweling/ToxTempAssistant) -* Bio.tools: [](https://bio.tools/) +* Bio.tools: Not available -* FAIRsharing: []() +* FAIRsharing: Not available -* TeSS: []() +* TeSS: Not available * RSD: [toxtempassistant](toxtempassistant) -* Wikipedia: []() +* Wikipedia: Not available - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000018 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000018](https://vhp4safety.github.io/glossary#VHP0000018) * Development Cloud: Not available @@ -70,7 +65,7 @@ An online application for implementation of weighted gene co-expression network ## Technical Tool Specifications -* Provider: Not available +* Provider: [Leiden University]() * Citation: [10.1007/s00204-021-03141-w](https://doi.org/10.1007/s00204-021-03141-w) @@ -82,7 +77,7 @@ An online application for implementation of weighted gene co-expression network * Docker: Not available -* Bio.tools: [TXG-MAPr](https://bio.tools/TXG-MAPr) +* Bio.tools: [TXG-MAPr](TXG-MAPr) * FAIRsharing: Not available @@ -102,6 +97,6 @@ An online application for implementation of weighted gene co-expression network "@id" : "https://vhp4safety.github.io/cloud/service/txg_mapr", "name": "TXG-MAPr", "description": "An online application for implementation of weighted gene co-expression network analysis (WGCNA) derived from publicly available transcriptomic datasets from the TG-GATEs database.", - "url": "" + "url": "https://txg-mapr.eu/" } diff --git a/docs/service/vhp_glossary.md b/docs/service/vhp_glossary.md index 0a94e375..feac3f7e 100644 --- a/docs/service/vhp_glossary.md +++ b/docs/service/vhp_glossary.md @@ -1,18 +1,13 @@ - # VHP4Safety Glossary - + A collection of ontology with names, abrreviations and definitions of the terminology that is used within the VHP4Safety project. - -**Main Webpage:** [https://glossary.vhp4safety.nl/](https://glossary.vhp4safety.nl/) - +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -41,13 +36,14 @@ A collection of ontology with names, abrreviations and definitions of the termin } } - + + ## VHP4Safety Service Metadata -* Stage: Other +* Stage: [Other](Other) -* Sub-Stage: Other +* Sub-stage: [Other](Other) * Development Cloud: Not available @@ -101,6 +97,6 @@ A collection of ontology with names, abrreviations and definitions of the termin "@id" : "https://vhp4safety.github.io/cloud/service/vhp_glossary", "name": "VHP4Safety Glossary", "description": "A collection of ontology with names, abrreviations and definitions of the terminology that is used within the VHP4Safety project.", - "url": "" + "url": "https://glossary.vhp4safety.nl/" } diff --git a/docs/service/wikibase.md b/docs/service/wikibase.md index 691d99d4..7231bbc2 100644 --- a/docs/service/wikibase.md +++ b/docs/service/wikibase.md @@ -1,22 +1,16 @@ - # VHP4Safety Wikibase - + A Wikibase instance for storing and presenting information about toxic, safe and potentially toxic compounds related to the VHP4Safety project. -![VHP4Safety Wikibase logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/wikibase.png) - -**Main Webpage:** [https://compoundcloud.wikibase.cloud/](https://compoundcloud.wikibase.cloud/) - +![VHP4Safety Wikibase logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/VHP4Safety_ChemicalCompounds.png) ## Documentation -#### VHP4Safety Documentation +* Service Introduction: [VHP4Safety Compound Wiki Overview](https://doi.org/10.5281/zenodo.13864849) -* Service Introduction: [VHP4Safety Compound Wiki Overview](https://doi.org/10.5281/zenodo.13864849) - -* Workflow: [Getting properties by SMILES using the VHP4Safety Compound Wiki](https://colab.research.google.com/drive/15Ea2N2CMxjVS2zMrvW2-R4vhsEqk8Shv) +* Workflow: [Getting properties by SMILES using the VHP4Safety Compound Wiki](https://colab.research.google.com/drive/15Ea2N2CMxjVS2zMrvW2-R4vhsEqk8Shv) * Demo: To be added @@ -42,13 +36,14 @@ A Wikibase instance for storing and presenting information about toxic, safe and } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000149 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000149](https://vhp4safety.github.io/glossary#VHP0000149) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000148](https://vhp4safety.github.io/glossary#VHP0000148) * Development Cloud: Not available @@ -70,7 +65,7 @@ A Wikibase instance for storing and presenting information about toxic, safe and ## Technical Tool Specifications -* Provider: Not available +* Provider: [Department of Translational Genomics, Maastricht University]() * Citation: [10.5281/zenodo.13864849](https://doi.org/10.5281/zenodo.13864849) @@ -102,6 +97,6 @@ A Wikibase instance for storing and presenting information about toxic, safe and "@id" : "https://vhp4safety.github.io/cloud/service/wikibase", "name": "VHP4Safety Wikibase", "description": "A Wikibase instance for storing and presenting information about toxic, safe and potentially toxic compounds related to the VHP4Safety project.", - "url": "" + "url": "https://compoundcloud.wikibase.cloud/" } diff --git a/docs/service/wikipathways_aop.md b/docs/service/wikipathways_aop.md index 3c00a209..95af6be9 100644 --- a/docs/service/wikipathways_aop.md +++ b/docs/service/wikipathways_aop.md @@ -1,19 +1,13 @@ - # WikiPathways - AOP Portal - + An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecular basis of AOPs and their key events (KEs). ![WikiPathways - AOP Portal logo](https://raw.githubusercontent.com/VHP4Safety/cloud/main/docs/service/wikipathways_aop.png) -**Main Webpage:** [https://aop.wikipathways.org/](https://aop.wikipathways.org/) - - ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,19 +36,20 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: []() +* Development Cloud: Not available * Login Required: No -* TRL: +* TRL: Not available * Type: internal @@ -74,15 +69,15 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu * Citation: [10.3389/fgene.2018.00661](https://doi.org/10.3389/fgene.2018.00661) -* Version: +* Version: Not available * License: [CC0](https://creativecommons.org/share-your-work/public-domain/cc0/) -* Source Code: []() +* Source Code: Not available -* Docker: []() +* Docker: Not available -* Bio.tools: [wikipathways](https://bio.tools/wikipathways) +* Bio.tools: [wikipathways](wikipathways) * FAIRsharing: Not available @@ -102,6 +97,6 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu "@id" : "https://vhp4safety.github.io/cloud/service/wikipathways_aop", "name": "WikiPathways - AOP Portal", "description": "An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecular basis of AOPs and their key events (KEs).", - "url": "" + "url": "https://aop.wikipathways.org/" } diff --git a/docs/service/xploreaop.md b/docs/service/xploreaop.md index 3152e04d..fb44c6d9 100644 --- a/docs/service/xploreaop.md +++ b/docs/service/xploreaop.md @@ -1,19 +1,13 @@ - # xploreaop - + A web application for visualization of Adverse Outcome Pathway (AOP) networks and interactive exploration of AOPs for two liver outcomes. - -**Main Webpage:** [https://xploreaop.cloud.vhp4safety.nl/](https://xploreaop.cloud.vhp4safety.nl/) - -**Tool Webpage:** [https://xploreaop.cloud.vhp4safety.nl/](https://xploreaop.cloud.vhp4safety.nl/) +No screenshot available. ## Documentation -#### VHP4Safety Documentation - * Service Introduction: To be added * Workflow: To be added @@ -42,15 +36,16 @@ A web application for visualization of Adverse Outcome Pathway (AOP) networks an } } - + + ## VHP4Safety Service Metadata -* Stage: https://vhp4safety.github.io/glossary#VHP0000102 +* Stage: [https://vhp4safety.github.io/glossary#VHP0000102](https://vhp4safety.github.io/glossary#VHP0000102) -* Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 +* Sub-stage: [https://vhp4safety.github.io/glossary#VHP0000023](https://vhp4safety.github.io/glossary#VHP0000023) -* Development Cloud: [https://xploreaop.cloud.vhp4safety.nl/](https://xploreaop.cloud.vhp4safety.nl/) +* Development Cloud: [https://xploreaop.cloud.vhp4safety.nl/](https://xploreaop.cloud.vhp4safety.nl/) * Login Required: Not available @@ -58,7 +53,7 @@ A web application for visualization of Adverse Outcome Pathway (AOP) networks an * Type: internal -* Contact: Not available +* Contact: Marc Teunis () * API Type: Not available @@ -70,7 +65,7 @@ A web application for visualization of Adverse Outcome Pathway (AOP) networks an ## Technical Tool Specifications -* Provider: Not available +* Provider: [Hogeschool Utrecht]() * Citation: Not available From 37645a162eea4adef29567e9aa220a6d35d872aa Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 3 Feb 2026 10:51:49 +0000 Subject: [PATCH 4/4] Generate method documentation from JSON files --- docs/methods/cell_titer_fluor.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/methods/cell_titer_fluor.md b/docs/methods/cell_titer_fluor.md index e25d09cc..aca7d1c4 100644 --- a/docs/methods/cell_titer_fluor.md +++ b/docs/methods/cell_titer_fluor.md @@ -1,4 +1,4 @@ -# [METHOD]: Cell Titer Fluor +# Cell Titer Fluor