diff --git a/bids2openminds/report.py b/bids2openminds/report.py index 5c1affb..440a158 100644 --- a/bids2openminds/report.py +++ b/bids2openminds/report.py @@ -9,20 +9,20 @@ def create_report(dataset, dataset_version, collection, dataset_description, inp behavioral_protocols_numbers = 0 for item in collection: - if item.type_ == "https://openminds.ebrains.eu/core/Subject": + if item.type_.endswith("Subject"): subject_number += 1 subject_state_numbers.append(len(item.studied_states)) - if item.type_ == "https://openminds.ebrains.eu/core/File": + if item.type_.endswith("File"): files_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/FileBundle": + if item.type_.endswith("FileBundle"): file_bundle_number += 1 - if item.type_ == "https://openminds.ebrains.eu/core/BehavioralProtocol": + if item.type_.endswith("BehavioralProtocol"): behavioral_protocols_numbers += 1 diff --git a/test/bids_examples_ds005.jsonld b/test/bids_examples_ds005.jsonld index a3793d4..b957b38 100644 --- a/test/bids_examples_ds005.jsonld +++ b/test/bids_examples_ds005.jsonld @@ -1,15 +1,15 @@ { "@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 }, @@ -17,20 +17,20 @@ "lookupLabel": "Studied state sub-01" }, { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year", - "@type": "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement", + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/year", + "@type": "https://openminds.om-i.org/types/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": [ { @@ -39,8 +39,8 @@ ] }, { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/male", - "@type": "https://openminds.ebrains.eu/controlledTerms/BiologicalSex", + "@id": "https://openminds.om-i.org/instances/biologicalSex/male", + "@type": "https://openminds.om-i.org/types/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", @@ -48,8 +48,8 @@ "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/PATO_0000384" }, { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens", - "@type": "https://openminds.ebrains.eu/controlledTerms/Species", + "@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", @@ -63,11 +63,11 @@ }, { "@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 +76,14 @@ }, { "@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": [ { @@ -92,8 +92,8 @@ ] }, { - "@id": "https://openminds.ebrains.eu/instances/biologicalSex/female", - "@type": "https://openminds.ebrains.eu/controlledTerms/BiologicalSex", + "@id": "https://openminds.om-i.org/instances/biologicalSex/female", + "@type": "https://openminds.om-i.org/types/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", @@ -102,11 +102,11 @@ }, { "@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 +115,14 @@ }, { "@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 +132,11 @@ }, { "@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 +145,14 @@ }, { "@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 +162,11 @@ }, { "@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 +175,14 @@ }, { "@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 +192,11 @@ }, { "@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 +205,14 @@ }, { "@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 +222,11 @@ }, { "@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 +235,14 @@ }, { "@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 +252,11 @@ }, { "@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 +265,14 @@ }, { "@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 +282,11 @@ }, { "@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 +295,14 @@ }, { "@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 +312,11 @@ }, { "@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 +325,14 @@ }, { "@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 +342,11 @@ }, { "@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 +355,14 @@ }, { "@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 +372,11 @@ }, { "@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 +385,14 @@ }, { "@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 +402,11 @@ }, { "@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 +415,14 @@ }, { "@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 +432,11 @@ }, { "@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 +445,14 @@ }, { "@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 +462,11 @@ }, { "@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 +475,14 @@ }, { "@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 +492,11 @@ }, { "@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 +505,14 @@ }, { "@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": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -522,849 +522,849 @@ }, { "@id": "_:000036", - "@type": "https://openminds.ebrains.eu/core/BehavioralProtocol", + "@type": "https://openminds.om-i.org/types/BehavioralProtocol", "description": "To be defined", "internalIdentifier": "mixedgamblestask", "name": "mixedgamblestask" }, { "@id": "_:000037", - "@type": "https://openminds.ebrains.eu/core/FileBundle", + "@type": "https://openminds.om-i.org/types/FileBundle", "contentDescription": "File bundle created for sub-12/anat", "isPartOf": { "@id": "_:000038" }, "name": "sub-12/anat", "storageSize": { - "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", + "@type": "https://openminds.om-i.org/types/QuantitativeValue", "unit": { - "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/byte" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/byte" } } }, { "@id": "_:000038", - 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"@type": "https://openminds.ebrains.eu/core/Person", + "@type": "https://openminds.om-i.org/types/Person", "familyName": "C.", "givenName": "Trepel" }, { "@id": "_:000228", - "@type": "https://openminds.ebrains.eu/core/Person", + "@type": "https://openminds.om-i.org/types/Person", "familyName": "R.A.", "givenName": "Poldrack" }, { "@id": "_:000229", - "@type": "https://openminds.ebrains.eu/core/DatasetVersion", + "@type": "https://openminds.om-i.org/types/DatasetVersion", "author": [ { "@id": "_:000225" @@ -5515,15 +5515,15 @@ ], "dataType": [ { - "@id": "https://openminds.ebrains.eu/instances/semanticDataType/rawData" + "@id": "https://openminds.om-i.org/instances/semanticDataType/rawData" } ], "experimentalApproach": [ { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/anatomy" + "@id": "https://openminds.om-i.org/instances/experimentalApproach/anatomy" }, { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/neuroimaging" + "@id": "https://openminds.om-i.org/instances/experimentalApproach/neuroimaging" } ], "fullName": "Mixed-gambles task", @@ -5583,18 +5583,18 @@ ], "technique": [ { - 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[adapted from [wikipedia](https://en.wikipedia.org/wiki/MRI_sequence)]", "name": "T2 pulse sequence", "synonym": [ @@ -5627,7 +5627,7 @@ }, { "@id": "_:000234", - "@type": "https://openminds.ebrains.eu/core/Dataset", + "@type": "https://openminds.om-i.org/types/Dataset", "author": [ { "@id": "_:000225" diff --git a/test/bids_examples_eeg_rest_fmri.jsonld b/test/bids_examples_eeg_rest_fmri.jsonld index 81e256d..3853ff0 100644 --- a/test/bids_examples_eeg_rest_fmri.jsonld +++ b/test/bids_examples_eeg_rest_fmri.jsonld @@ -1,21 +1,21 @@ { "@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", "internalIdentifier": "Studied state sub-32", "lookupLabel": "Studied state sub-32" }, { "@id": "_:000001", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "internalIdentifier": "sub-32", "lookupLabel": "sub-32", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -23,33 +23,19 @@ } ] }, - { - "@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": "_:000003", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "internalIdentifier": "Studied state sub-35", "lookupLabel": "Studied state sub-35" }, { "@id": "_:000004", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "internalIdentifier": "sub-35", "lookupLabel": "sub-35", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -59,17 +45,17 @@ }, { "@id": "_:000005", - "@type": "https://openminds.ebrains.eu/core/SubjectState", + "@type": "https://openminds.om-i.org/types/SubjectState", "internalIdentifier": "Studied state sub-36", "lookupLabel": "Studied state sub-36" }, { "@id": "_:000006", - "@type": "https://openminds.ebrains.eu/core/Subject", + "@type": "https://openminds.om-i.org/types/Subject", "internalIdentifier": "sub-36", "lookupLabel": "sub-36", "species": { - "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens" + "@id": "https://openminds.om-i.org/instances/species/homoSapiens" }, "studiedState": [ { @@ -79,554 +65,518 @@ }, { "@id": "_:000007", - 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"@id": "https://openminds.ebrains.eu/instances/experimentalApproach/neuroimaging" + "@id": "https://openminds.om-i.org/instances/experimentalApproach/neuroimaging" }, { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/neuralConnectivity" + "@id": "https://openminds.om-i.org/instances/experimentalApproach/anatomy" } ], "fullName": "EEG, fMRI and NODDI at rest'", @@ -1875,21 +1819,61 @@ ], "technique": [ { - "@id": "https://openminds.ebrains.eu/instances/technique/diffusionWeightedImaging" + "@id": "https://openminds.om-i.org/instances/technique/diffusionWeightedImaging" }, { - "@id": "https://openminds.ebrains.eu/instances/technique/electroencephalography" + "@id": "https://openminds.om-i.org/instances/technique/electroencephalography" } ] }, { - "@id": "https://openminds.ebrains.eu/instances/semanticDataType/rawData", - "@type": "https://openminds.ebrains.eu/controlledTerms/SemanticDataType", - "name": "raw data" + "@id": "_:000093", + "@type": "https://openminds.om-i.org/types/Dataset", + "author": [ + { + "@id": "_:000079" + }, + { + "@id": "_:000080" + }, + { + "@id": "_:000081" + }, + { + "@id": "_:000082" + }, + { + "@id": "_:000083" + }, + { + "@id": "_:000084" + } + ], + "fullName": "EEG, fMRI and NODDI at rest'", + "hasVersion": [ + { + "@id": "_:000085" + } + ], + "shortName": "EEG, fMRI and NODDI at rest'" }, { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/anatomy", - "@type": "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach", + "@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", @@ -1899,69 +1883,62 @@ ] }, { - "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/electrophysiology", - "@type": "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach", + "@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.ebrains.eu/instances/experimentalApproach/neuroimaging", - "@type": "https://openminds.ebrains.eu/controlledTerms/ExperimentalApproach", + "@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.ebrains.eu/instances/experimentalApproach/neuralConnectivity", - "@type": "https://openminds.ebrains.eu/controlledTerms/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/semanticDataType/rawData", + "@type": "https://openminds.om-i.org/types/SemanticDataType", + "name": "raw data" }, { - "@id": "https://openminds.ebrains.eu/instances/technique/diffusionWeightedImaging", - "@type": "https://openminds.ebrains.eu/controlledTerms/Technique", + "@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.ebrains.eu/instances/technique/electroencephalography", - "@type": "https://openminds.ebrains.eu/controlledTerms/Technique", + "@id": "https://openminds.om-i.org/instances/technique/electroencephalography", + "@type": "https://openminds.om-i.org/types/Technique", "name": "electroencephalography" }, { - "@id": "_:000094", - "@type": "https://openminds.ebrains.eu/core/Dataset", - "author": [ - { - "@id": "_:000080" - }, - { - "@id": "_:000081" - }, - { - "@id": "_:000082" - }, - { - "@id": "_:000083" - }, - { - "@id": "_:000084" - }, - { - "@id": "_:000085" - } - ], - "fullName": "EEG, fMRI and NODDI at rest'", - "hasVersion": [ - { - "@id": "_:000086" - } - ], - "shortName": "EEG, fMRI and NODDI at rest'" + "@id": "https://openminds.om-i.org/instances/unitOfMeasurement/byte", + "@type": "https://openminds.om-i.org/types/UnitOfMeasurement", + "name": "byte" } ] } diff --git a/test/test_bids_examples.py b/test/test_bids_examples.py index 6ceaeb2..b47d20a 100644 --- a/test/test_bids_examples.py +++ b/test/test_bids_examples.py @@ -6,12 +6,12 @@ # Dataset information in following order dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number, dataset_file_bundles_number, dataset_behavioral_protocol_number example_dataset = [("ds003", 13, 13, 2, 58, 39, 1), - ("ds000247", 6, 10, 5, 202, 41, 2), + ("ds000247", 6, 10, 5, 50, 41, 2), # The authors list in 'eeg_cbm' contains non person entities 2 is not correct name (issue raied #43) ("eeg_cbm", 20, 20, 2, 104, 40, 1), ("asl001", 1, 1, 2, 8, 3, 0), # Number of files in 'eeg_rest_fmri' is not correct as it doesn't contain files in derivated (issue raied #42) - ("eeg_rest_fmri", 3, 3, 6, 46, 22, 1)] + ("eeg_rest_fmri", 3, 3, 6, 45, 22, 1)] @pytest.mark.parametrize("dataset_label, dataset_subject_number, dataset_subject_state_number, dataset_person_number, dataset_files_number, dataset_file_bundles_number, dataset_behavioral_protocol_number", example_dataset) @@ -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_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_subject_age.py b/test/test_subject_age.py index 96b0bb0..2ead5b4 100644 --- a/test/test_subject_age.py +++ b/test/test_subject_age.py @@ -6,16 +6,16 @@ (45, "QuantitativeValue"), ("XX", None)] -@ pytest.mark.parametrize("age,age_type", example_ages) +@pytest.mark.parametrize("age,age_type", example_ages) 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 9360221..b3516aa 100644 --- a/test/test_thorough_bids_example.py +++ b/test/test_thorough_bids_example.py @@ -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