[ENH] Update JSONLD examples with @context and outputs from bagel derivatives

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": {

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