diff --git a/bids2openminds/main.py b/bids2openminds/main.py index 3c2ea3f..77ae924 100644 --- a/bids2openminds/main.py +++ b/bids2openminds/main.py @@ -6,8 +6,8 @@ import pandas as pd from nameparser import HumanName -import openminds.v3.core as omcore -import openminds.v3.controlled_terms as controlled_terms +import openminds.v4.core as omcore +import openminds.v4.controlled_terms as controlled_terms from openminds import IRI from .utility import table_filter, pd_table_value, file_hash, file_storage_size, detect_nifti_version diff --git a/bids2openminds/utility.py b/bids2openminds/utility.py index 7311a9d..756a2c3 100644 --- a/bids2openminds/utility.py +++ b/bids2openminds/utility.py @@ -7,9 +7,9 @@ import pandas as pd -import openminds.v3.controlled_terms as controlled_terms -from openminds.v3.core import Hash, QuantitativeValue, ContentType -from openminds.v3.controlled_terms import UnitOfMeasurement +import openminds.v4.controlled_terms as controlled_terms +from openminds.v4.core import Hash, QuantitativeValue, ContentType +from openminds.v4.controlled_terms import UnitOfMeasurement def read_json(file_path: str) -> dict: diff --git a/test/bids_examples_ds005.jsonld b/test/bids_examples_ds005.jsonld index a3793d4..e4f9467 100644 --- a/test/bids_examples_ds005.jsonld +++ b/test/bids_examples_ds005.jsonld @@ -1,36 +1,31 @@ { "@context": { - "@vocab": "https://openminds.ebrains.eu/vocab/" + "@vocab": "https://openminds.om-i.org/props/" }, "@graph": [ { "@id": "_:000000", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 28 }, "internalIdentifier": "Studied state sub-01", "lookupLabel": "Studied state sub-01" }, - { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year", - "@type": "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement", - "name": "year" - }, { "@id": "_:000002", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-01", "lookupLabel": "sub-01", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -38,36 +33,13 @@ } ] }, - { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male", - "@type": "https://openminds.ebrains.eu/controlledTerms/BiologicalSex", - "definition": "Biological sex that produces sperm cells (spermatozoa).", - "description": "A male organism typically has the capacity to produce relatively small, usually mobile gametes (reproductive cells), called sperm cells (or spermatozoa). In the process of fertilization, these sperm cells fuse with a larger, usually immobile female gamete, called egg cell (or ovum).", - "interlexIdentifier": "http://uri.interlex.org/base/ilx_0106489", - "name": "male", - "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/PATO_0000384" - }, - { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens", - "@type": "https://openminds.ebrains.eu/controlledTerms/Species", - "definition": "The species *Homo sapiens* (humans) belongs to the family of *hominidae* (great apes).", - "interlexIdentifier": "http://uri.interlex.org/base/ilx_0105114", - "knowledgeSpaceLink": "https://knowledge-space.org/wiki/NCBITaxon:9606#human", - "name": "Homo sapiens", - "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "synonym": [ - "homo sapien", - "human", - "man" - ] - }, { "@id": "_:000005", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 21 }, @@ -76,14 +48,14 @@ }, { "@id": "_:000006", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-02", "lookupLabel": "sub-02", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -91,22 +63,13 @@ } ] }, - { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female", - "@type": "https://openminds.ebrains.eu/controlledTerms/BiologicalSex", - "definition": "Biological sex that produces egg cells (ova).", - "description": "A female organism typically has the capacity to produce relatively large, usually immobile gametes (reproductive cells), called egg cells (or ova). In the process of fertilization, an egg cell (ovum) fuses with a smaller, usually mobile male gametes, called sperm cells (or spermatozoa).", - "interlexIdentifier": "http://uri.interlex.org/base/ilx_0104150", - "name": "female", - "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/PATO_0000383" - }, { "@id": "_:000008", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 27 }, @@ -115,14 +78,14 @@ }, { "@id": "_:000009", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-03", "lookupLabel": "sub-03", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -132,11 +95,11 @@ }, { "@id": "_:000010", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 25 }, @@ -145,14 +108,14 @@ }, { "@id": "_:000011", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-04", "lookupLabel": "sub-04", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -162,11 +125,11 @@ }, { "@id": "_:000012", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 20 }, @@ -175,14 +138,14 @@ }, { "@id": "_:000013", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-05", "lookupLabel": "sub-05", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -192,11 +155,11 @@ }, { "@id": "_:000014", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 20 }, @@ -205,14 +168,14 @@ }, { "@id": "_:000015", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-06", "lookupLabel": "sub-06", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -222,11 +185,11 @@ }, { "@id": "_:000016", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 24 }, @@ -235,14 +198,14 @@ }, { "@id": "_:000017", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-07", "lookupLabel": "sub-07", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -252,11 +215,11 @@ }, { "@id": "_:000018", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 25 }, @@ -265,14 +228,14 @@ }, { "@id": "_:000019", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-08", "lookupLabel": "sub-08", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -282,11 +245,11 @@ }, { "@id": "_:000020", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 19 }, @@ -295,14 +258,14 @@ }, { "@id": "_:000021", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-09", "lookupLabel": "sub-09", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -312,11 +275,11 @@ }, { "@id": "_:000022", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 20 }, @@ -325,14 +288,14 @@ }, { "@id": "_:000023", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-10", "lookupLabel": "sub-10", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -342,11 +305,11 @@ }, { "@id": "_:000024", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 20 }, @@ -355,14 +318,14 @@ }, { "@id": "_:000025", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-11", "lookupLabel": "sub-11", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -372,11 +335,11 @@ }, { "@id": "_:000026", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 21 }, @@ -385,14 +348,14 @@ }, { "@id": "_:000027", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-12", "lookupLabel": "sub-12", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -402,11 +365,11 @@ }, { "@id": "_:000028", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 22 }, @@ -415,14 +378,14 @@ }, { "@id": "_:000029", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-13", "lookupLabel": "sub-13", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -432,11 +395,11 @@ }, { "@id": "_:000030", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 19 }, @@ -445,14 +408,14 @@ }, { "@id": "_:000031", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-14", "lookupLabel": "sub-14", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -462,11 +425,11 @@ }, { "@id": "_:000032", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 20 }, @@ -475,14 +438,14 @@ }, { "@id": "_:000033", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female" + "@id": "https://openminds.om-i.org/instances/biologicalSex/female" }, "internalIdentifier": "sub-15", "lookupLabel": "sub-15", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -492,11 +455,11 @@ }, { "@id": "_:000034", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "age": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year" }, "value": 22 }, @@ -505,14 +468,14 @@ }, { "@id": "_:000035", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "biologicalSex": { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male" + "@id": "https://openminds.om-i.org/instances/biologicalSex/male" }, "internalIdentifier": "sub-16", "lookupLabel": "sub-16", "species": { - 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"interlexIdentifier": "http://uri.interlex.org/base/ilx_0739411", - "name": "anatomy", - "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Anatomy", - "synonym": [ - "anatomical approach" - ] - }, - { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/electrophysiology", - "@type": "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach", - "definition": "Any experimental approach focused on electrical phenomena associated with living systems, most notably the nervous system, cardiac system, and musculoskeletal system.", - "interlexIdentifier": "http://uri.interlex.org/base/ilx_0741202", - "name": "electrophysiology", - "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Electrophysiology" - }, - { - "@id": "https://openminds.ebrains.eu/instances/technique/diffusionWeightedImaging", - "@type": "https://openminds.ebrains.eu/controlledTerms/Technique", - "name": "diffusion-weighted imaging" - }, - { - "@id": "https://openminds.ebrains.eu/instances/technique/electroencephalography", - "@type": "https://openminds.ebrains.eu/controlledTerms/Technique", - "name": "electroencephalography" - }, { "@id": "_:000093", - "@type": "https://openminds.ebrains.eu/core/Dataset", + "@type": "https://openminds.om-i.org/types/Dataset", "author": [ { "@id": "_:000079" @@ -1939,6 +1880,89 @@ } ], "shortName": "EEG, fMRI and NODDI at rest'" + }, + { + "@id": "https://openminds.om-i.org/instances/contentTypes/application_vnd.bids", + "@type": "https://openminds.om-i.org/types/ContentType", + "name": "application/vnd.bids", + "synonym": [ + "BIDS" + ] + }, + { + "@id": "https://openminds.om-i.org/instances/dataType/voxelData", + "@type": "https://openminds.om-i.org/types/DataType", + "definition": "'Voxel data' is a matrix defining values (scalars, lists, or matrices) on a grid in a three dimensional space, which can be rendered to raster graphic.", + "name": "voxel data" + }, + { + "@id": "https://openminds.om-i.org/instances/experimentalApproach/anatomy", + "@type": "https://openminds.om-i.org/types/ExperimentalApproach", + "definition": "Any experimental approach focused on the bodily structure of living organisms.", + "interlexIdentifier": "http://uri.interlex.org/base/ilx_0739411", + "name": "anatomy", + "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Anatomy", + "synonym": [ + "anatomical approach" + ] + }, + { + "@id": "https://openminds.om-i.org/instances/experimentalApproach/electrophysiology", + "@type": "https://openminds.om-i.org/types/ExperimentalApproach", + "definition": "Any experimental approach focused on electrical phenomena associated with living systems, most notably the nervous system, cardiac system, and musculoskeletal system.", + "interlexIdentifier": "http://uri.interlex.org/base/ilx_0741202", + "name": "electrophysiology", + "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Electrophysiology" + }, + { + "@id": "https://openminds.om-i.org/instances/experimentalApproach/neuralConnectivity", + "@type": "https://openminds.om-i.org/types/ExperimentalApproach", + "definition": "Any experimental approach focused on functional or anatomical connections between single neurons or populations of neurons in defined anatomical regions.", + "interlexIdentifier": "http://uri.interlex.org/base/ilx_0739393", + "name": "neural connectivity", + "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Connectivity" + }, + { + "@id": "https://openminds.om-i.org/instances/experimentalApproach/neuroimaging", + "@type": "https://openminds.om-i.org/types/ExperimentalApproach", + "definition": "Any experimental approach focused on the non-invasive direct or indirect imaging of the structure, function, or pharmacology of the nervous system.", + "interlexIdentifier": "http://uri.interlex.org/base/ilx_0741206", + "name": "neuroimaging", + "preferredOntologyIdentifier": "http://uri.interlex.org/tgbugs/uris/readable/modality/Neuroimaging" + }, + { + "@id": "https://openminds.om-i.org/instances/semanticDataType/rawData", + "@type": "https://openminds.om-i.org/types/SemanticDataType", + "name": "raw data" + }, + { + "@id": "https://openminds.om-i.org/instances/species/homoSapiens", + "@type": "https://openminds.om-i.org/types/Species", + "definition": "The species *Homo sapiens* (humans) belongs to the family of *hominidae* (great apes).", + "interlexIdentifier": "http://uri.interlex.org/base/ilx_0105114", + "knowledgeSpaceLink": "https://knowledge-space.org/wiki/NCBITaxon:9606#human", + "name": "Homo sapiens", + "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_9606", + "synonym": [ + "homo sapien", + "human", + "man" + ] + }, + { + "@id": "https://openminds.om-i.org/instances/technique/diffusionWeightedImaging", + "@type": "https://openminds.om-i.org/types/Technique", + "name": "diffusion-weighted imaging" + }, + { + "@id": "https://openminds.om-i.org/instances/technique/electroencephalography", + "@type": "https://openminds.om-i.org/types/Technique", + "name": "electroencephalography" + }, + { + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/byte", + "@type": "https://openminds.om-i.org/types/UnitOfMeasurement", + "name": "byte" } ] -} +} \ No newline at end of file diff --git a/test/test_bids_examples.py b/test/test_bids_examples.py index 71d92de..064f1b8 100644 --- a/test/test_bids_examples.py +++ b/test/test_bids_examples.py @@ -19,7 +19,7 @@ def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject test_dir = os.path.join("bids-examples", dataset_label) bids2openminds.converter.convert(test_dir, save_output=True) c = Collection() - c.load(os.path.join(test_dir, "openminds.jsonld"), version="v3") + c.load(os.path.join(test_dir, "openminds.jsonld"), version="v4") subject_number = 0 subject_state_number = 0 @@ -30,18 +30,18 @@ def test_example_datasets(dataset_label, dataset_subject_number, dataset_subject subject_state_number_besed_on_subject = 0 for item in c: - if item.type_ == "https://openminds.ebrains.eu/core/Subject": + if item.type_ == "https://openminds.om-i.org/types/Subject": subject_number += 1 subject_state_number_besed_on_subject += len(item.studied_states) - if item.type_ == "https://openminds.ebrains.eu/core/SubjectState": + if item.type_ == "https://openminds.om-i.org/types/SubjectState": subject_state_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/Person": + if item.type_ == "https://openminds.om-i.org/types/Person": person_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/File": + if item.type_ == "https://openminds.om-i.org/types/File": files_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/FileBundle": + if item.type_ == "https://openminds.om-i.org/types/FileBundle": file_bundles_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/BehavioralProtocol": + if item.type_ == "https://openminds.om-i.org/types/BehavioralProtocol": behavioral_protocol_number += 1 assert dataset_subject_number == subject_number diff --git a/test/test_example_datasets_click.py b/test/test_example_datasets_click.py index 8b476ad..6eef09c 100644 --- a/test/test_example_datasets_click.py +++ b/test/test_example_datasets_click.py @@ -13,7 +13,7 @@ def test_example_datasets_click(): result = runner.invoke(convert_click, [test_dir]) assert result.exit_code == 0 c = Collection() - c.load(os.path.join(test_dir, "openminds.jsonld"), version="v3") + c.load(os.path.join(test_dir, "openminds.jsonld"), version="v4") def test_example_datasets_click_seperate_files(): @@ -36,4 +36,4 @@ def test_example_datasets_click_output_location(): convert_click, ["-o", openminds_file, test_dir]) assert result.exit_code == 0 c = Collection() - c.load(openminds_file, version="v3") + c.load(openminds_file, version="v4") diff --git a/test/test_file_bundle.py b/test/test_file_bundle.py index 7becca5..847dd08 100644 --- a/test/test_file_bundle.py +++ b/test/test_file_bundle.py @@ -50,7 +50,7 @@ def test_number_file_bundle(generate_file_bundle_collection): _, collection, _ = generate_file_bundle_collection m = 0 for item in collection: - if item.type_ == "https://openminds.ebrains.eu/core/FileBundle": + if item.type_ == "https://openminds.om-i.org/types/FileBundle": m += 1 assert m == number_of_openminds_bundle @@ -82,7 +82,7 @@ def test_random_folder(test_dir, path_list, bundle, parent_bundle, generate_file dataset_bundle = None for item in collection: - if item.type_ == "https://openminds.ebrains.eu/core/FileBundle" and item.name == folder_name: + if item.type_ == "https://openminds.om-i.org/types/FileBundle" and item.name == folder_name: # detects only one file bundle have this name assert dataset_bundle is None dataset_bundle = item @@ -94,5 +94,5 @@ def test_random_folder(test_dir, path_list, bundle, parent_bundle, generate_file if parent_bundle is not None: assert dataset_bundle.is_part_of.name == parent_bundle[0] else: - assert dataset_bundle.is_part_of.type_ == "https://openminds.ebrains.eu/core/FileRepository" + assert dataset_bundle.is_part_of.type_ == "https://openminds.om-i.org/types/FileRepository" assert dataset_bundle.is_part_of.iri.value == file_repository_iri diff --git a/test/test_person.py b/test/test_person.py index 6dd5371..de33198 100644 --- a/test/test_person.py +++ b/test/test_person.py @@ -1,7 +1,7 @@ # test for create_openminds_person function in the main import pytest from bids2openminds.main import create_openminds_person -import openminds.v3.core as omcore +import openminds.v4.core as omcore # Test data: (full_name, given_name, family_name) example_names = [("John Ronald Reuel Tolkien", "John Ronald Reuel", "Tolkien"), diff --git a/test/test_subject_age.py b/test/test_subject_age.py index 96b0bb0..1c43ab0 100644 --- a/test/test_subject_age.py +++ b/test/test_subject_age.py @@ -11,11 +11,11 @@ def test_subject_age(age, age_type): data_subject_table = pd.DataFrame(data={'age': [age]}) openminds_age = create_openminds_age(data_subject_table) if age_type == "QuantitativeValueRange": - assert openminds_age.type_ == 'https://openminds.ebrains.eu/core/QuantitativeValueRange' + assert openminds_age.type_ == 'https://openminds.om-i.org/types/QuantitativeValueRange' assert openminds_age.max_value is None assert openminds_age.min_value == 89 if age_type == "QuantitativeValue": - assert openminds_age.type_ == 'https://openminds.ebrains.eu/core/QuantitativeValue' + assert openminds_age.type_ == 'https://openminds.om-i.org/types/QuantitativeValue' assert openminds_age.value == age if age_type == None: assert openminds_age is None diff --git a/test/test_thorough_bids_example.py b/test/test_thorough_bids_example.py index 5514ed5..d071633 100644 --- a/test/test_thorough_bids_example.py +++ b/test/test_thorough_bids_example.py @@ -31,12 +31,12 @@ def load_collections(): file.write(actual_data) reference_collection = Collection() - reference_collection.load(tempdir+test_standard_name, version="v3") + reference_collection.load(tempdir+test_standard_name, version="v4") bids2openminds.converter.convert(test_dataset, save_output=True) generated_collection = Collection() generated_collection.load(os.path.join( - test_dataset, "openminds.jsonld"), version="v3") + test_dataset, "openminds.jsonld"), version="v4") collections[dataset_label] = ( reference_collection, generated_collection) @@ -46,7 +46,7 @@ def load_collections(): def detect_type(collection, type): - type_IRI = "https://openminds.ebrains.eu/core/" + type + type_IRI = "https://openminds.om-i.org/types/" + type items_list = [] for item in collection: if item.type_ == type_IRI: @@ -164,6 +164,6 @@ def test_file_bundle(load_collections, dataset_label): generated_file_bundle = find_name( refrence_file_bundle.name, generated_file_bundles) assert generated_file_bundle is not None - if refrence_file_bundle.is_part_of.type_ == "https://openminds.ebrains.eu/core/FileBundle": - assert generated_file_bundle.is_part_of.type_ == "https://openminds.ebrains.eu/core/FileBundle" + if refrence_file_bundle.is_part_of.type_ == "https://openminds.om-i.org/types/FileBundle": + assert generated_file_bundle.is_part_of.type_ == "https://openminds.om-i.org/types/FileBundle" assert refrence_file_bundle.is_part_of.name == generated_file_bundle.is_part_of.name