[ENH][BEP028] Specification update for BEP028 BIDS-Prov

mkdocs.yml

@@ -10,6 +10,7 @@ nav:
           - Data summary files: modality-agnostic-files/data-summary-files.md
           - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
           - Code: modality-agnostic-files/code.md
+          - Provenance: modality-agnostic-files/provenance.md
           - Events: modality-agnostic-files/events.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md

src/introduction.md

@@ -192,6 +192,15 @@ For example:
     Scientific Data 12, (13841).
     [doi:10.1038/s41597-025-05543-2](https://doi.org/10.1038/s41597-025-05543-2)
 
+### Other extensions specific publications
+
+#### Provenance
+
+-   Rémi Adon, Stefan Appelhoff, Tibor Auer, Laurent Guillo, Yaroslav O Halchenko, David Keator, Christopher J Markiewicz, Thomas E Nichols, Jean-Baptiste Poline, Satrajit Ghosh, Camille Maumet (2021).
+    **BIDS-prov: a provenance framework for BIDS**.
+    OHBM 2021 - 25th Annual Meeting of the Organization for Human Brain Mapping, Jun 2021, Online, South Korea. pp.1-3
+    [https://inserm.hal.science/inserm-03478998v1](https://inserm.hal.science/inserm-03478998v1)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a

src/modality-agnostic-files/dataset-description.md

@@ -45,17 +45,6 @@ and a guide for using macros can be found at
    }
 ) }}
 
-Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-<!-- This block generates a table describing subfields within a metadata field.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
-
 Example:
 
 ```JSON
@@ -107,8 +96,6 @@ Example:
 }
 ```
 
-### Derived dataset and pipeline description
-
 As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline-name>/dataset_description.json`.

src/modality-agnostic-files/provenance-context.json

@@ -0,0 +1,48 @@
+{
+    "@context": {
+        "prov" : "http://www.w3.org/ns/prov#",
+        "xsd": "http://www.w3.org/2001/XMLSchema#",
+        "RRID": "http://scicrunch.org/resolver/",
+        "Id": "@id",
+        "Type": "@type",
+        "Label": "http://www.w3.org/2000/01/rdf-schema#label",
+        "StartedAtTime" : {
+          "@id": "prov:startedAtTime",
+          "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
+        },
+        "EndedAtTime" : {
+          "@id": "prov:endedAtTime",
+          "@type": "xsd:dateTime"
+        },
+        "GeneratedBy" : {
+          "@id": "prov:wasGeneratedBy",
+          "@type": "@id"
+        },
+        "AttributedTo" : {
+          "@id": "prov:wasAttributedTo",
+          "@type": "@id"
+        },
+        "AssociatedWith" : {
+          "@id": "prov:wasAssociatedWith",
+          "@type": "@id"
+        },
+        "InformedBy" : {
+          "@id": "prov:wasInformedBy",
+          "@type": "@id"
+        },
+        "Used" : {
+          "@id": "prov:used",
+          "@type": "@id"
+        },
+        "ActedOnBehalfOf" : {
+          "@id": "prov:actedOnBehalfOf",
+          "@type": "@id"
+        },
+        "Entities": "prov:Entity",
+        "Entity": "prov:Entity",
+        "Activities": "prov:Activity",
+        "Activity": "prov:Activity",
+        "Software": "prov:SoftwareAgent",
+        "Atlocation": "prov:atLocation"
+    }
+}