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[MNT] Regenerate example annotated JSON and JSONLDs using SNOMED asse…
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…ssments (#49)

* replace CogAtlas terms with SNOMED ones

* regenerate JSONLD files with SNOMED assessment terms
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@alyssadai
alyssadai authored Dec 19, 2024
1 parent 872d2ca commit 5690cd4
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Showing 5 changed files with 255 additions and 259 deletions.
12 changes: 6 additions & 6 deletions data-upload/example_synthetic.json
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Original file line number Diff line number Diff line change
Expand Up @@ -95,8 +95,8 @@
"Label": "Assessment tool"
},
"IsPartOf": {
"TermURL": "cogatlas:trm_57964b8a66aed",
"Label": "Montreal Cognitive Assessment"
"TermURL": "snomed:859351000000102",
"Label": "Montreal cognitive assessment"
},
"MissingValues": [
"missing"
Expand All @@ -111,8 +111,8 @@
"Label": "Assessment tool"
},
"IsPartOf": {
"TermURL": "cogatlas:trm_57964b8a66aed",
"Label": "Montreal Cognitive Assessment"
"TermURL": "snomed:859351000000102",
"Label": "Montreal cognitive assessment"
},
"MissingValues": [
"missing"
Expand All @@ -127,8 +127,8 @@
"Label": "Assessment tool"
},
"IsPartOf": {
"TermURL": "cogatlas:tsk_4a57abb949ece",
"Label": "Unified Parkinson's Disease Rating Scale"
"TermURL": "snomed:342061000000106",
"Label": "Unified Parkinsons disease rating scale score"
},
"MissingValues": [
"not completed"
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69 changes: 34 additions & 35 deletions data-upload/example_synthetic.jsonld
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
{
"@context": {
"cogatlas": "https://www.cognitiveatlas.org/task/id/",
"nb": "http://neurobagel.org/vocab/",
"ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
"nidm": "http://purl.org/nidash/nidm#",
Expand Down Expand Up @@ -70,16 +69,16 @@
},
"SubjectGroup": "nb:SubjectGroup"
},
"identifier": "nb:838f54dd-bc3c-4469-8795-b5e280ae0f82",
"identifier": "nb:925a0d0c-7b16-47a2-8505-6fabcc18a68c",
"hasLabel": "BIDS synthetic",
"hasPortalURI": "https://github.com/bids-standard/bids-examples",
"hasSamples": [
{
"identifier": "nb:f8e8d12d-50fd-40f8-8805-ddf5a3913a36",
"identifier": "nb:1bdb1187-63a5-4b7b-99d8-f8820b313245",
"hasLabel": "sub-01",
"hasSession": [
{
"identifier": "nb:bcdb7b7f-be17-402b-bc20-c3a374a43431",
"identifier": "nb:87639b4f-d36c-4388-9f8f-c337787046bf",
"hasLabel": "ses-01",
"hasAge": 34.1,
"hasSex": {
Expand All @@ -92,18 +91,18 @@
},
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
"schemaKey": "PhenotypicSession"
},
{
"identifier": "nb:3d0464fa-918a-474a-ad40-7d730a002031",
"identifier": "nb:44d9b3dd-f01f-42b9-bdab-f127dbd530e9",
"hasLabel": "ses-02",
"hasAge": 35.3,
"hasSex": {
Expand All @@ -116,11 +115,11 @@
},
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
Expand All @@ -130,11 +129,11 @@
"schemaKey": "Subject"
},
{
"identifier": "nb:c73690c0-37d9-4ef9-8d55-e71e3fc16f0a",
"identifier": "nb:65148792-3dc4-4926-a719-c614e87b17f3",
"hasLabel": "sub-02",
"hasSession": [
{
"identifier": "nb:92d61f79-2331-4273-a4b6-0d8e9045f09b",
"identifier": "nb:8bfc9bd2-224e-4383-8f82-11d1731f8bac",
"hasLabel": "ses-01",
"hasSex": {
"identifier": "snomed:248153007",
Expand All @@ -148,18 +147,18 @@
],
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
"schemaKey": "PhenotypicSession"
},
{
"identifier": "nb:3c42b3dc-cbd4-4f11-968b-a90a0e3af294",
"identifier": "nb:6d5e37c0-966b-41a8-9454-c0a5616cfaba",
"hasLabel": "ses-02",
"hasAge": 39.0,
"hasSex": {
Expand All @@ -174,11 +173,11 @@
],
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
Expand All @@ -188,23 +187,23 @@
"schemaKey": "Subject"
},
{
"identifier": "nb:885389cd-6b66-45ff-b0a7-7028b66a5fc8",
"identifier": "nb:9a1a5c81-2e7f-4f03-a523-bcaa0ead4a39",
"hasLabel": "sub-03",
"hasSession": [
{
"identifier": "nb:7e580649-68d5-4a7a-8518-ace5906b751a",
"identifier": "nb:23686b31-623b-482b-b406-971088f03fdd",
"hasLabel": "ses-01",
"hasAge": 22.1,
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
}
],
"schemaKey": "PhenotypicSession"
},
{
"identifier": "nb:8b90bf80-1765-496a-9a2f-9c31a52fe35e",
"identifier": "nb:762b54f6-feae-4311-89c3-f38e326ebb32",
"hasLabel": "ses-02",
"hasAge": 23.2,
"hasDiagnosis": [
Expand All @@ -215,11 +214,11 @@
],
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
Expand All @@ -229,11 +228,11 @@
"schemaKey": "Subject"
},
{
"identifier": "nb:232f9e9a-fc3b-48e5-9d57-9d64492c35f4",
"identifier": "nb:7a8f3df4-4bee-42b1-9118-4093a3f9910c",
"hasLabel": "sub-04",
"hasSession": [
{
"identifier": "nb:d0236a6c-b16d-4ff8-9878-10e8219aeb8a",
"identifier": "nb:61107ff4-971a-4edf-91fd-1b9d170b0e22",
"hasLabel": "ses-01",
"hasAge": 21.1,
"hasSex": {
Expand All @@ -246,14 +245,14 @@
},
"hasAssessment": [
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
"schemaKey": "PhenotypicSession"
},
{
"identifier": "nb:d138e635-72fb-4eb2-9080-d33ff60a868d",
"identifier": "nb:0b08fab5-3a54-438b-b5ec-ec68f81cb423",
"hasLabel": "ses-02",
"hasAge": 22.3,
"hasSex": {
Expand All @@ -266,11 +265,11 @@
},
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
Expand All @@ -280,11 +279,11 @@
"schemaKey": "Subject"
},
{
"identifier": "nb:25f83242-227f-486a-b21a-7ca9f509c718",
"identifier": "nb:1663eca7-e148-4db5-bc4b-cd73995a1c90",
"hasLabel": "sub-05",
"hasSession": [
{
"identifier": "nb:b5cff3ea-570e-40c5-81f8-2f2d6fdd4d7e",
"identifier": "nb:ef0ddc83-3584-4c05-9166-9f72f32683d7",
"hasLabel": "ses-01",
"hasAge": 42.5,
"hasSex": {
Expand All @@ -299,18 +298,18 @@
],
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
"schemaKey": "PhenotypicSession"
},
{
"identifier": "nb:8de97991-183c-4a08-a174-71d4f4d0e629",
"identifier": "nb:464d03b4-ca11-4ca9-a5f5-f4a5308aa6bd",
"hasLabel": "ses-02",
"hasAge": 43.2,
"hasSex": {
Expand All @@ -325,11 +324,11 @@
],
"hasAssessment": [
{
"identifier": "cogatlas:trm_57964b8a66aed",
"identifier": "snomed:859351000000102",
"schemaKey": "Assessment"
},
{
"identifier": "cogatlas:tsk_4a57abb949ece",
"identifier": "snomed:342061000000106",
"schemaKey": "Assessment"
}
],
Expand Down
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