From 485d692b464fc67aefc0f31da9622332f21bd4ff Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Tue, 1 Oct 2024 21:49:00 -0400 Subject: [PATCH 1/3] regenerate bagel pheno & bids example outputs with updated context --- data-upload/example_synthetic.jsonld | 50 +++--- .../example_synthetic_pheno-bids.jsonld | 150 ++++++++++-------- 2 files changed, 112 insertions(+), 88 deletions(-) diff --git a/data-upload/example_synthetic.jsonld b/data-upload/example_synthetic.jsonld index 937951b..33e9a49 100644 --- a/data-upload/example_synthetic.jsonld +++ b/data-upload/example_synthetic.jsonld @@ -1,10 +1,11 @@ { "@context": { - "nb": "http://neurobagel.org/vocab/", - "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/", - "nidm": "http://purl.org/nidash/nidm#", "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#", + "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/", + "np": "https://github.com/nipoppy/pipeline-catalog/tree/main/processing", "Acquisition": "nb:Acquisition", "identifier": "@id", "hasContrastType": { @@ -14,6 +15,13 @@ "Assessment": "nb:Assessment", "Bagel": "nb:Bagel", "BaseModel": "nb:BaseModel", + "CompletedPipeline": "nb:CompletedPipeline", + "hasPipelineVersion": { + "@id": "nb:hasPipelineVersion" + }, + "hasPipelineName": { + "@id": "nb:hasPipelineName" + }, "ControlledTerm": "nb:ControlledTerm", "Dataset": "nb:Dataset", "hasLabel": { @@ -34,6 +42,9 @@ "hasAcquisition": { "@id": "nb:hasAcquisition" }, + "hasCompletedPipeline": { + "@id": "nb:hasCompletedPipeline" + }, "PhenotypicSession": "nb:PhenotypicSession", "hasAge": { "@id": "nb:hasAge" @@ -50,6 +61,7 @@ "hasAssessment": { "@id": "nb:hasAssessment" }, + "Pipeline": "nb:Pipeline", "Session": "nb:Session", "Sex": "nb:Sex", "Subject": "nb:Subject", @@ -58,16 +70,16 @@ }, "SubjectGroup": "nb:SubjectGroup" }, - "identifier": "nb:e0c7d08c-edcc-4c2a-816a-306878ed7be2", + "identifier": "nb:d49a2c52-5c06-4a93-8c98-f451bcb0b4ac", "hasLabel": "BIDS synthetic", "hasPortalURI": "https://github.com/bids-standard/bids-examples", "hasSamples": [ { - "identifier": "nb:34ec1e2d-9a81-4a50-bcd0-eb22c88d11e1", + "identifier": "nb:9808824d-079b-4507-a592-30a74b0f8930", "hasLabel": "sub-01", "hasSession": [ { - "identifier": "nb:85c7473c-6122-4999-ad3b-5cd57a883c87", + "identifier": "nb:20ac92dd-5f2d-406f-9146-4ee23c3a10fb", "hasLabel": "ses-01", "hasAge": 34.1, "hasSex": { @@ -91,7 +103,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:eb57d0c1-fb96-4c04-8c16-1f29f7f40db4", + "identifier": "nb:5721e7e7-52ac-411c-99a6-aa88e34d2bd9", "hasLabel": "ses-02", "hasAge": 35.3, "hasSex": { @@ -118,11 +130,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:2de41397-805f-4059-b464-388ef501d6e5", + "identifier": "nb:278421eb-9c38-4506-bb1c-750f04dc6f6f", "hasLabel": "sub-02", "hasSession": [ { - "identifier": "nb:0ce182f3-b47c-4b50-8b76-8f257e490cf3", + "identifier": "nb:54558db8-8d9d-4cfb-a6da-1db75579d183", "hasLabel": "ses-01", "hasSex": { "identifier": "snomed:248153007", @@ -147,7 +159,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:4871d5c2-963f-4825-ab43-85a87edac4ce", + "identifier": "nb:120ec371-ee81-4c95-a8e6-02f728a90d7f", "hasLabel": "ses-02", "hasAge": 39.0, "hasSex": { @@ -176,11 +188,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:d4258426-2971-43ff-92fa-4b20bd21c31f", + "identifier": "nb:868cfd33-af43-402d-90ec-8c7abb6cceef", "hasLabel": "sub-03", "hasSession": [ { - "identifier": "nb:3f9c82d5-6648-4b9b-8f86-195ee9283875", + "identifier": "nb:eabfeb08-511c-4edc-81ab-8373da1c62ae", "hasLabel": "ses-01", "hasAge": 22.1, "hasAssessment": [ @@ -192,7 +204,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:0f7fe93b-13b1-4ca7-9e58-b997a18ec9b9", + "identifier": "nb:a1230dae-825e-4c2a-bfac-81739f1c908d", "hasLabel": "ses-02", "hasAge": 23.2, "hasDiagnosis": [ @@ -217,11 +229,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:73193f71-cd19-4b8c-ae73-abc882e9b688", + "identifier": "nb:8055cea8-96a4-4ee6-9a8b-18fe3c5c722e", "hasLabel": "sub-04", "hasSession": [ { - "identifier": "nb:962aa986-dbd7-4412-a180-49c0a24c9f87", + "identifier": "nb:9fb642ce-dbdf-4aa5-bf42-dc53133984fd", "hasLabel": "ses-01", "hasAge": 21.1, "hasSex": { @@ -241,7 +253,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:8622fc66-013d-4675-a328-fdcccd4616b0", + "identifier": "nb:10f6b6af-8ab7-426f-8cda-3492380f60bd", "hasLabel": "ses-02", "hasAge": 22.3, "hasSex": { @@ -268,11 +280,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:cb8d7a96-fdec-425c-b0b5-9e9ac3c70e8c", + "identifier": "nb:b4dcce1c-da3e-4b4e-b7d7-151266fc7843", "hasLabel": "sub-05", "hasSession": [ { - "identifier": "nb:1d7c30f5-cae9-43c9-a154-26dbe0029594", + "identifier": "nb:d28a095d-4d1d-4532-a2b0-9d4497d68853", "hasLabel": "ses-01", "hasAge": 42.5, "hasSex": { @@ -298,7 +310,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:2401e418-6f9b-4113-9511-b1b9a332a5d0", + "identifier": "nb:e4a922f9-73bf-42df-aa8e-a016cc2e543e", "hasLabel": "ses-02", "hasAge": 43.2, "hasSex": { diff --git a/data-upload/pheno-bids-output/example_synthetic_pheno-bids.jsonld b/data-upload/pheno-bids-output/example_synthetic_pheno-bids.jsonld index 44e7f6d..ec921fb 100644 --- a/data-upload/pheno-bids-output/example_synthetic_pheno-bids.jsonld +++ b/data-upload/pheno-bids-output/example_synthetic_pheno-bids.jsonld @@ -1,10 +1,11 @@ { "@context": { - "nb": "http://neurobagel.org/vocab/", - "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/", - "nidm": "http://purl.org/nidash/nidm#", "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#", + "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/", + "np": "https://github.com/nipoppy/pipeline-catalog/tree/main/processing", "Acquisition": "nb:Acquisition", "identifier": "@id", "hasContrastType": { @@ -14,6 +15,13 @@ "Assessment": "nb:Assessment", "Bagel": "nb:Bagel", "BaseModel": "nb:BaseModel", + "CompletedPipeline": "nb:CompletedPipeline", + "hasPipelineVersion": { + "@id": "nb:hasPipelineVersion" + }, + "hasPipelineName": { + "@id": "nb:hasPipelineName" + }, "ControlledTerm": "nb:ControlledTerm", "Dataset": "nb:Dataset", "hasLabel": { @@ -34,6 +42,9 @@ "hasAcquisition": { "@id": "nb:hasAcquisition" }, + "hasCompletedPipeline": { + "@id": "nb:hasCompletedPipeline" + }, "PhenotypicSession": "nb:PhenotypicSession", "hasAge": { "@id": "nb:hasAge" @@ -50,6 +61,7 @@ "hasAssessment": { "@id": "nb:hasAssessment" }, + "Pipeline": "nb:Pipeline", "Session": "nb:Session", "Sex": "nb:Sex", "Subject": "nb:Subject", @@ -58,16 +70,16 @@ }, "SubjectGroup": "nb:SubjectGroup" }, - "identifier": "nb:e0c7d08c-edcc-4c2a-816a-306878ed7be2", + "identifier": "nb:d49a2c52-5c06-4a93-8c98-f451bcb0b4ac", "hasLabel": "BIDS synthetic", "hasPortalURI": "https://github.com/bids-standard/bids-examples", "hasSamples": [ { - "identifier": "nb:34ec1e2d-9a81-4a50-bcd0-eb22c88d11e1", + "identifier": "nb:9808824d-079b-4507-a592-30a74b0f8930", "hasLabel": "sub-01", "hasSession": [ { - "identifier": "nb:85c7473c-6122-4999-ad3b-5cd57a883c87", + "identifier": "nb:20ac92dd-5f2d-406f-9146-4ee23c3a10fb", "hasLabel": "ses-01", "hasAge": 34.1, "hasSex": { @@ -91,7 +103,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:eb57d0c1-fb96-4c04-8c16-1f29f7f40db4", + "identifier": "nb:5721e7e7-52ac-411c-99a6-aa88e34d2bd9", "hasLabel": "ses-02", "hasAge": 35.3, "hasSex": { @@ -115,12 +127,12 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:e67fd08b-9bf9-4ed8-b4cc-d0142cd27789", + "identifier": "nb:8e9a8a7c-62ed-46a5-bd77-0d9f3167066e", "hasLabel": "ses-01", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01", "hasAcquisition": [ { - "identifier": "nb:5dc2e11e-4f7a-4b0e-9488-843f0a607f4b", + "identifier": "nb:2b329f71-3d5f-4d8b-8aff-fd59897c25a4", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -128,7 +140,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:3436fd9f-9895-4282-9990-42537e0e3365", + "identifier": "nb:5488fe9d-9716-427a-9a6c-7f4a7ab93fe1", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -136,7 +148,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:b65e635a-29eb-4de2-9d9a-4d1940ff65c7", + "identifier": "nb:793af0cf-fe52-41f1-a2ac-e50c3b256216", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -144,7 +156,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:0709012b-6b83-435d-b332-6dbbf8ef48c7", + "identifier": "nb:182d83a2-86a8-426d-908c-81f5e2cf0320", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -155,12 +167,12 @@ "schemaKey": "ImagingSession" }, { - "identifier": "nb:66177197-51e0-403c-bbfb-806b123f243d", + "identifier": "nb:df025d76-b354-42fb-abb7-1a4c244d9261", "hasLabel": "ses-02", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02", "hasAcquisition": [ { - "identifier": "nb:368ca74f-c4cd-4d46-a856-67e0f3634d45", + "identifier": "nb:e7c0ef3d-bb57-4854-abb6-1ce0d857af71", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -168,7 +180,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:eebd46f0-1d9c-428c-8e30-91115fb02952", + "identifier": "nb:7d5e6ae8-5d03-45bd-938b-d63975533065", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -176,7 +188,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:49444dbf-f56e-4fec-a096-77e3f71a3a8a", + "identifier": "nb:d7d8531f-5ec0-46a3-9075-94ee366f82be", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -184,7 +196,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:b5e79c41-d953-4de0-b038-85c20d16dd08", + "identifier": "nb:b68e5d64-a4d1-4060-9800-72dd7a2cb1c2", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -198,11 +210,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:2de41397-805f-4059-b464-388ef501d6e5", + "identifier": "nb:278421eb-9c38-4506-bb1c-750f04dc6f6f", "hasLabel": "sub-02", "hasSession": [ { - "identifier": "nb:0ce182f3-b47c-4b50-8b76-8f257e490cf3", + "identifier": "nb:54558db8-8d9d-4cfb-a6da-1db75579d183", "hasLabel": "ses-01", "hasSex": { "identifier": "snomed:248153007", @@ -227,7 +239,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:4871d5c2-963f-4825-ab43-85a87edac4ce", + "identifier": "nb:120ec371-ee81-4c95-a8e6-02f728a90d7f", "hasLabel": "ses-02", "hasAge": 39.0, "hasSex": { @@ -253,12 +265,12 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:63d093bd-62df-42f5-86b7-210258f67c9b", + "identifier": "nb:60fa9b5e-8d77-42bc-8fd5-24af7e53ceb8", "hasLabel": "ses-01", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01", "hasAcquisition": [ { - "identifier": "nb:41dc7ce3-959a-480a-8e6f-aff312384b87", + "identifier": "nb:2126733c-a983-4647-b3cf-c7c7f977cf7f", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -266,7 +278,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:1ba90704-000c-46c1-bb02-eb5e7ac45751", + "identifier": "nb:703655a4-21db-462a-b4ab-0d176f558e31", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -274,7 +286,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:a531d16e-7d55-4909-8d7d-1b4af6d8b914", + "identifier": "nb:63506697-0fa3-47e5-b0e9-0a6e52a02ca9", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -282,7 +294,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f4e9ba66-64e4-46b5-b92f-1a428b9d9f15", + "identifier": "nb:f2c4ec85-5d6e-4342-b792-9beecd34f600", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -293,12 +305,12 @@ "schemaKey": "ImagingSession" }, { - "identifier": "nb:e17501bb-216f-487a-99f5-491f18f60ad5", + "identifier": "nb:5aeeea44-1c01-4a38-a75a-6f850d260c91", "hasLabel": "ses-02", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-02", "hasAcquisition": [ { - "identifier": "nb:f0ed98eb-6639-4014-98bd-25e75b72da06", + "identifier": "nb:4be14fe0-b935-4f47-aa07-32706c63054d", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -306,7 +318,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f5ecb749-d807-4213-a318-f35ef9bdb17a", + "identifier": "nb:017140f3-b3d4-4c88-b98b-91784eed174e", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -314,7 +326,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:4290daa5-c9c9-4aa3-a289-3d4d43798e1f", + "identifier": "nb:cfa21fd9-faab-46b6-a75b-406a9e47d68d", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -322,7 +334,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:3b691219-511f-4fcf-9837-241432a78db8", + "identifier": "nb:d5fc2b6d-06f0-4ee8-b343-7226921ca078", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -336,11 +348,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:d4258426-2971-43ff-92fa-4b20bd21c31f", + "identifier": "nb:868cfd33-af43-402d-90ec-8c7abb6cceef", "hasLabel": "sub-03", "hasSession": [ { - "identifier": "nb:3f9c82d5-6648-4b9b-8f86-195ee9283875", + "identifier": "nb:eabfeb08-511c-4edc-81ab-8373da1c62ae", "hasLabel": "ses-01", "hasAge": 22.1, "hasAssessment": [ @@ -352,7 +364,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:0f7fe93b-13b1-4ca7-9e58-b997a18ec9b9", + "identifier": "nb:a1230dae-825e-4c2a-bfac-81739f1c908d", "hasLabel": "ses-02", "hasAge": 23.2, "hasDiagnosis": [ @@ -374,12 +386,12 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:32660b2a-e5e8-4e1b-af5c-4c5cdacce21d", + "identifier": "nb:725db190-d772-4d8f-ba8d-3eed0b18114a", "hasLabel": "ses-01", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-01", "hasAcquisition": [ { - "identifier": "nb:f9c90ddb-5e7f-40f5-b195-666054c0176c", + "identifier": "nb:fd9de041-93f0-4490-aee9-b059fec4e38b", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -387,7 +399,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:3691a8f3-8f7d-47f1-a014-1a5dd69b1ee6", + "identifier": "nb:25d477dc-7770-44e9-b70f-27542d314223", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -395,7 +407,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:4be1fbcd-62a2-497b-9f12-4d6a069a8449", + "identifier": "nb:1a620a34-cc7b-424b-86af-bfce34f753b4", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -403,7 +415,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:aea0110e-da1f-4f7e-b424-39e159fd137f", + "identifier": "nb:2414b473-432c-4515-92da-a09cb15787b6", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -414,12 +426,12 @@ "schemaKey": "ImagingSession" }, { - "identifier": "nb:12a5131a-d8ee-4e4c-bb4c-f39aa755b03c", + "identifier": "nb:31712e5e-9e25-468e-ac72-14ee050565bc", "hasLabel": "ses-02", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-02", "hasAcquisition": [ { - "identifier": "nb:ca11ecc9-773b-4496-b63c-8cfc23ca9a78", + "identifier": "nb:393e0d5f-764e-40a3-9432-7b0fc5d12f4e", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -427,7 +439,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f8b246c2-1eb5-4821-b244-b511d7d86a25", + "identifier": "nb:ecfc2277-3542-4451-9918-a3fe9aa86313", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -435,7 +447,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:8b238169-cc99-484e-8869-02c4008719e3", + "identifier": "nb:f42bb90e-6380-4f96-8c8d-e4e2d9b06c20", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -443,7 +455,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:3ece5f2b-2c5a-48e2-9bd6-41b12c4d317e", + "identifier": "nb:3a33893b-a20a-406b-aa6e-c5bf90ae458d", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -457,11 +469,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:73193f71-cd19-4b8c-ae73-abc882e9b688", + "identifier": "nb:8055cea8-96a4-4ee6-9a8b-18fe3c5c722e", "hasLabel": "sub-04", "hasSession": [ { - "identifier": "nb:962aa986-dbd7-4412-a180-49c0a24c9f87", + "identifier": "nb:9fb642ce-dbdf-4aa5-bf42-dc53133984fd", "hasLabel": "ses-01", "hasAge": 21.1, "hasSex": { @@ -481,7 +493,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:8622fc66-013d-4675-a328-fdcccd4616b0", + "identifier": "nb:10f6b6af-8ab7-426f-8cda-3492380f60bd", "hasLabel": "ses-02", "hasAge": 22.3, "hasSex": { @@ -505,12 +517,12 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:4c4ad446-2dfa-447b-8982-0e89252a48db", + "identifier": "nb:d5664739-b1d0-4e02-b186-fbc754cecb65", "hasLabel": "ses-01", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01", "hasAcquisition": [ { - "identifier": "nb:055cbbe8-cb3b-4ce4-bf44-6872d6abf8c8", + "identifier": "nb:8004f940-2653-4d28-a67c-d8f6985d3e51", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -518,7 +530,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:e110bf95-6855-43c3-a675-05b486510ad7", + "identifier": "nb:209fdf7c-4898-407f-94bf-0439e010ab9c", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -526,7 +538,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:afcba6b2-266c-4a1d-9c35-4629fc28f0fe", + "identifier": "nb:e9a58abb-a821-48cf-b889-83b3966c5da2", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -534,7 +546,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f2aae326-dbbd-4d84-bc4a-1c390a6aff55", + "identifier": "nb:16c0adeb-66df-45ea-9b70-9ad60e09c9c7", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -545,12 +557,12 @@ "schemaKey": "ImagingSession" }, { - "identifier": "nb:e799e71d-5378-4c58-8cad-66a827fa6a6d", + "identifier": "nb:1d2d426d-1fee-4d0d-ae19-91657f79f901", "hasLabel": "ses-02", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02", "hasAcquisition": [ { - "identifier": "nb:4bdedf63-eb73-4fe0-bf29-c439e331d475", + "identifier": "nb:d6dfd07d-2db2-42aa-a21f-2ebeac650661", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -558,7 +570,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:21b162d2-b025-4a3d-95f6-e65b35639a3e", + "identifier": "nb:d172c672-d2f5-4b24-bfd9-27a1b8978f49", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -566,7 +578,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f78ad803-ac7e-4951-b68c-56448b2da336", + "identifier": "nb:4d43f63c-f400-4dff-9026-5a91b9371bb1", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -574,7 +586,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:0fd038f4-5fc6-4811-ad32-c333e3066724", + "identifier": "nb:2c4a9210-8a32-4bcf-a368-0bb8601c7ea1", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -588,11 +600,11 @@ "schemaKey": "Subject" }, { - "identifier": "nb:cb8d7a96-fdec-425c-b0b5-9e9ac3c70e8c", + "identifier": "nb:b4dcce1c-da3e-4b4e-b7d7-151266fc7843", "hasLabel": "sub-05", "hasSession": [ { - "identifier": "nb:1d7c30f5-cae9-43c9-a154-26dbe0029594", + "identifier": "nb:d28a095d-4d1d-4532-a2b0-9d4497d68853", "hasLabel": "ses-01", "hasAge": 42.5, "hasSex": { @@ -618,7 +630,7 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:2401e418-6f9b-4113-9511-b1b9a332a5d0", + "identifier": "nb:e4a922f9-73bf-42df-aa8e-a016cc2e543e", "hasLabel": "ses-02", "hasAge": 43.2, "hasSex": { @@ -644,12 +656,12 @@ "schemaKey": "PhenotypicSession" }, { - "identifier": "nb:b1c3704d-787e-42d8-9b7a-e80309938136", + "identifier": "nb:e818df98-22ca-40d0-97a1-c49a27470d61", "hasLabel": "ses-01", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-01", "hasAcquisition": [ { - "identifier": "nb:5db67199-752a-44e5-bcad-89405e0b7c22", + "identifier": "nb:a1fb071b-de24-4a17-ae31-bcf66458fd44", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -657,7 +669,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:85e7525b-9d56-467d-b81e-e9668a10b313", + "identifier": "nb:afbd3be2-28a6-460c-90b9-6cf88151304b", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -665,7 +677,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:38f8440c-bc52-4aed-bee5-84a8d43cb1fc", + "identifier": "nb:4fd13271-6664-4762-ac2b-741dd98e9a2e", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -673,7 +685,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:08b41711-4bba-4cfe-bd2e-bc9b3353f59a", + "identifier": "nb:ff0042aa-9ba9-47ec-804e-23b3cf80b5b3", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -684,12 +696,12 @@ "schemaKey": "ImagingSession" }, { - "identifier": "nb:85881582-f817-4f8c-b8e2-aa7781180bfe", + "identifier": "nb:64eaaa71-c448-4944-bf18-1b5b399b4c98", "hasLabel": "ses-02", "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-02", "hasAcquisition": [ { - "identifier": "nb:a2efc296-46a7-468b-a9a0-cf091517424d", + "identifier": "nb:2146af6c-3456-4953-9581-6387317a7275", "hasContrastType": { "identifier": "nidm:T1Weighted", "schemaKey": "Image" @@ -697,7 +709,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:143c340a-728a-4711-8929-131b84ea5f4f", + "identifier": "nb:7cc066e2-216c-46d0-a706-8b470c2946c0", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -705,7 +717,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:2f6f5949-df23-42c0-befd-b9365eb33621", + "identifier": "nb:6c602c8c-f862-4683-b9b4-1a417bb41fa3", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" @@ -713,7 +725,7 @@ "schemaKey": "Acquisition" }, { - "identifier": "nb:f492c69b-d101-4f27-a2cd-6e1cb34f24ef", + "identifier": "nb:a7e0af24-35b1-4a24-8bc3-1eb3a6f6b7f6", "hasContrastType": { "identifier": "nidm:FlowWeighted", "schemaKey": "Image" From 1be0a4249731f4a3dde913bdf76dc38ac962753f Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Tue, 1 Oct 2024 21:52:58 -0400 Subject: [PATCH 2/3] add example outputs from the bagel derivatives command --- ...le_synthetic_pheno-bids-derivatives.jsonld | 794 ++++++++++++++++++ ...example_synthetic_pheno-derivatives.jsonld | 409 +++++++++ 2 files changed, 1203 insertions(+) create mode 100644 data-upload/pheno-bids-derivatives-output/example_synthetic_pheno-bids-derivatives.jsonld create mode 100644 data-upload/pheno-derivatives-output/example_synthetic_pheno-derivatives.jsonld diff --git a/data-upload/pheno-bids-derivatives-output/example_synthetic_pheno-bids-derivatives.jsonld b/data-upload/pheno-bids-derivatives-output/example_synthetic_pheno-bids-derivatives.jsonld new file mode 100644 index 0000000..9ee5ff9 --- /dev/null +++ b/data-upload/pheno-bids-derivatives-output/example_synthetic_pheno-bids-derivatives.jsonld @@ -0,0 +1,794 @@ +{ + "@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#", + "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/", + "np": "https://github.com/nipoppy/pipeline-catalog/tree/main/processing", + "Acquisition": "nb:Acquisition", + "identifier": "@id", + "hasContrastType": { + "@id": "nb:hasContrastType" + }, + "schemaKey": "@type", + "Assessment": "nb:Assessment", + "Bagel": "nb:Bagel", + "BaseModel": "nb:BaseModel", + "CompletedPipeline": "nb:CompletedPipeline", + "hasPipelineVersion": { + "@id": "nb:hasPipelineVersion" + }, + "hasPipelineName": { + "@id": "nb:hasPipelineName" + }, + "ControlledTerm": "nb:ControlledTerm", + "Dataset": "nb:Dataset", + "hasLabel": { + "@id": "nb:hasLabel" + }, + "hasPortalURI": { + "@id": "nb:hasPortalURI" + }, + "hasSamples": { + "@id": "nb:hasSamples" + }, + "Diagnosis": "nb:Diagnosis", + "Image": "nb:Image", + "ImagingSession": "nb:ImagingSession", + "hasFilePath": { + "@id": "nb:hasFilePath" + }, + "hasAcquisition": { + "@id": "nb:hasAcquisition" + }, + "hasCompletedPipeline": { + "@id": "nb:hasCompletedPipeline" + }, + "PhenotypicSession": "nb:PhenotypicSession", + "hasAge": { + "@id": "nb:hasAge" + }, + "hasSex": { + "@id": "nb:hasSex" + }, + "isSubjectGroup": { + "@id": "nb:isSubjectGroup" + }, + "hasDiagnosis": { + "@id": "nb:hasDiagnosis" + }, + "hasAssessment": { + "@id": "nb:hasAssessment" + }, + "Pipeline": "nb:Pipeline", + "Session": "nb:Session", + "Sex": "nb:Sex", + "Subject": "nb:Subject", + "hasSession": { + "@id": "nb:hasSession" + }, + "SubjectGroup": "nb:SubjectGroup" + }, + "identifier": "nb:e0c7d08c-edcc-4c2a-816a-306878ed7be2", + "hasLabel": "BIDS synthetic", + "hasPortalURI": "https://github.com/bids-standard/bids-examples", + "hasSamples": [ + { + "identifier": "nb:34ec1e2d-9a81-4a50-bcd0-eb22c88d11e1", + "hasLabel": "sub-01", + "hasSession": [ + { + "identifier": "nb:85c7473c-6122-4999-ad3b-5cd57a883c87", + "hasLabel": "ses-01", + "hasAge": 34.1, + "hasSex": { + "identifier": "snomed:248152002", + "schemaKey": "Sex" + }, + "isSubjectGroup": { + "identifier": "ncit:C94342", + "schemaKey": "SubjectGroup" + }, + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:eb57d0c1-fb96-4c04-8c16-1f29f7f40db4", + "hasLabel": "ses-02", + "hasAge": 35.3, + "hasSex": { + "identifier": "snomed:248152002", + "schemaKey": "Sex" + }, + "isSubjectGroup": { + "identifier": "ncit:C94342", + "schemaKey": "SubjectGroup" + }, + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:e67fd08b-9bf9-4ed8-b4cc-d0142cd27789", + "hasLabel": "ses-01", + "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01", + "hasAcquisition": [ + { + "identifier": "nb:5dc2e11e-4f7a-4b0e-9488-843f0a607f4b", + "hasContrastType": { + "identifier": "nidm:T1Weighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:3436fd9f-9895-4282-9990-42537e0e3365", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:b65e635a-29eb-4de2-9d9a-4d1940ff65c7", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:0709012b-6b83-435d-b332-6dbbf8ef48c7", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + } + ], + "hasCompletedPipeline": [ + { + "identifier": "nb:f337b293-7302-44e0-b1c0-62bf2a21684c", + "hasPipelineVersion": "23.1.3", + "hasPipelineName": { + "identifier": "np:fmriprep", + "schemaKey": "Pipeline" + }, + "schemaKey": "CompletedPipeline" + }, + { + "identifier": "nb:64e96fc6-e95b-46b4-919d-b0f8f4e0c080", + "hasPipelineVersion": "7.3.2", + "hasPipelineName": { + "identifier": "np:freesurfer", + "schemaKey": "Pipeline" + }, + "schemaKey": "CompletedPipeline" + } + ], + "schemaKey": "ImagingSession" + }, + { + "identifier": "nb:66177197-51e0-403c-bbfb-806b123f243d", + "hasLabel": "ses-02", + "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02", + "hasAcquisition": [ + { + "identifier": "nb:368ca74f-c4cd-4d46-a856-67e0f3634d45", + "hasContrastType": { + "identifier": "nidm:T1Weighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:eebd46f0-1d9c-428c-8e30-91115fb02952", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:49444dbf-f56e-4fec-a096-77e3f71a3a8a", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:b5e79c41-d953-4de0-b038-85c20d16dd08", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + } + ], + "schemaKey": "ImagingSession" + } + ], + "schemaKey": "Subject" + }, + { + "identifier": "nb:2de41397-805f-4059-b464-388ef501d6e5", + "hasLabel": "sub-02", + "hasSession": [ + { + "identifier": "nb:0ce182f3-b47c-4b50-8b76-8f257e490cf3", + "hasLabel": "ses-01", + "hasSex": { + "identifier": "snomed:248153007", + "schemaKey": "Sex" + }, + "hasDiagnosis": [ + { + "identifier": "snomed:406506008", + "schemaKey": "Diagnosis" + } + ], + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:4871d5c2-963f-4825-ab43-85a87edac4ce", + "hasLabel": "ses-02", + "hasAge": 39.0, + "hasSex": { + "identifier": "snomed:248153007", + "schemaKey": "Sex" + }, + "hasDiagnosis": [ + { + "identifier": "snomed:406506008", + "schemaKey": "Diagnosis" + } + ], + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:63d093bd-62df-42f5-86b7-210258f67c9b", + "hasLabel": "ses-01", + "hasFilePath": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01", + "hasAcquisition": [ + { + "identifier": "nb:41dc7ce3-959a-480a-8e6f-aff312384b87", + "hasContrastType": { + "identifier": "nidm:T1Weighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:1ba90704-000c-46c1-bb02-eb5e7ac45751", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:a531d16e-7d55-4909-8d7d-1b4af6d8b914", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": 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"schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:f5ecb749-d807-4213-a318-f35ef9bdb17a", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:4290daa5-c9c9-4aa3-a289-3d4d43798e1f", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + }, + { + "identifier": "nb:3b691219-511f-4fcf-9837-241432a78db8", + "hasContrastType": { + "identifier": "nidm:FlowWeighted", + "schemaKey": "Image" + }, + "schemaKey": "Acquisition" + } + ], + "hasCompletedPipeline": [ + { + "identifier": "nb:52641a26-9a63-4c26-bb39-bffef9952f59", + "hasPipelineVersion": "7.3.2", + "hasPipelineName": { + "identifier": "np:freesurfer", + "schemaKey": "Pipeline" + }, + "schemaKey": "CompletedPipeline" + } + ], + "schemaKey": "ImagingSession" + } + ], + "schemaKey": "Subject" + }, + { + "identifier": 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"nb:73193f71-cd19-4b8c-ae73-abc882e9b688", + "hasLabel": "sub-04", + "hasSession": [ + { + "identifier": "nb:962aa986-dbd7-4412-a180-49c0a24c9f87", + "hasLabel": "ses-01", + "hasAge": 21.1, + "hasSex": { + "identifier": "snomed:248152002", + "schemaKey": "Sex" + }, + "isSubjectGroup": { + "identifier": "ncit:C94342", + "schemaKey": "SubjectGroup" + }, + "hasAssessment": [ + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:8622fc66-013d-4675-a328-fdcccd4616b0", + "hasLabel": "ses-02", + "hasAge": 22.3, + "hasSex": { + "identifier": "snomed:248152002", + "schemaKey": "Sex" + }, + "isSubjectGroup": { + "identifier": "ncit:C94342", + "schemaKey": "SubjectGroup" + }, + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + } + ], + "schemaKey": "Subject" + }, + { + "identifier": "nb:cb8d7a96-fdec-425c-b0b5-9e9ac3c70e8c", + "hasLabel": "sub-05", + "hasSession": [ + { + "identifier": "nb:1d7c30f5-cae9-43c9-a154-26dbe0029594", + "hasLabel": "ses-01", + "hasAge": 42.5, + "hasSex": { + "identifier": "snomed:248153007", + "schemaKey": "Sex" + }, + "hasDiagnosis": [ + { + "identifier": "snomed:406506008", + "schemaKey": "Diagnosis" + } + ], + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + }, + { + "identifier": "nb:2401e418-6f9b-4113-9511-b1b9a332a5d0", + "hasLabel": "ses-02", + "hasAge": 43.2, + "hasSex": { + "identifier": "snomed:248153007", + "schemaKey": "Sex" + }, + "hasDiagnosis": [ + { + "identifier": "snomed:406506008", + "schemaKey": "Diagnosis" + } + ], + "hasAssessment": [ + { + "identifier": "cogatlas:trm_57964b8a66aed", + "schemaKey": "Assessment" + }, + { + "identifier": "cogatlas:tsk_4a57abb949ece", + "schemaKey": "Assessment" + } + ], + "schemaKey": "PhenotypicSession" + } + ], + "schemaKey": "Subject" + } + ], + "schemaKey": "Dataset" +} \ No newline at end of file From bfa0998b5195f7266754e09d7b77c13312496c98 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Tue, 1 Oct 2024 22:01:19 -0400 Subject: [PATCH 3/3] add proc status file corresponding to BIDS synthetic dataset --- data-upload/nipoppy_proc_status_synthetic.tsv | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 data-upload/nipoppy_proc_status_synthetic.tsv diff --git a/data-upload/nipoppy_proc_status_synthetic.tsv b/data-upload/nipoppy_proc_status_synthetic.tsv new file mode 100644 index 0000000..e2bc680 --- /dev/null +++ b/data-upload/nipoppy_proc_status_synthetic.tsv @@ -0,0 +1,9 @@ +participant_id bids_participant session_id bids_session pipeline_name pipeline_version pipeline_step status +01 sub-01 01 ses-01 fmriprep 20.2.7 step1 FAIL +01 sub-01 01 ses-01 fmriprep 20.2.7 step2 INCOMPLETE +01 sub-01 01 ses-01 fmriprep 23.1.3 default SUCCESS +01 sub-01 01 ses-01 freesurfer 7.3.2 default SUCCESS +01 sub-01 02 ses-02 freesurfer 7.3.2 default UNAVAILABLE +02 sub-02 01 ses-01 fmriprep 23.1.3 default SUCCESS +02 sub-02 01 ses-01 freesurfer 7.3.2 default SUCCESS +02 sub-02 02 ses-02 freesurfer 7.3.2 default SUCCESS