bids-standard · bclenet · Jun 19, 2025 · Jun 19, 2025 · Jun 19, 2025 · Jun 19, 2025
diff --git a/mkdocs.yml b/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
@@ -125,6 +126,9 @@ markdown_extensions:
         - name: tsvgz
           class: tsv
           format: !!python/name:bidsschematools.render.tsv.fence
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
   - admonition
   - pymdownx.details
 plugins:

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -9,7 +9,7 @@
     "remark-lint-no-trailing-spaces": "^4.0.3",
     "remark-preset-lint-markdown-style-guide": "^6.0.1",
     "remark-preset-lint-recommended": "^7.0.1",
-    "prettier": "^3.7.4",
+    "prettier": "^3.8.0",
     "all-contributors-cli": "^6.26.1"
   }
 }
@@ -979,10 +979,10 @@ Bare DOIs such as `10.18112/openneuro.ds000001.v1.0.0` are [DEPRECATED][].
 
 ### BIDS URI
 
-To reference files in BIDS datasets, the following URI scheme may be used:
+To reference files or directories in BIDS datasets, the following URI scheme may be used:
 
 ```plain
-bids:[<dataset-name>]:<relative-path>
+bids:[<dataset-name>]:<relative-path>[#<fragment>]
 ```
 
 The scheme component `bids` identifies a BIDS URI,
@@ -991,18 +991,25 @@ The `dataset-name` component is an identifier for a BIDS dataset,
 and the `relative-path` component is the location of a resource within that
 BIDS dataset, relative to the root of that dataset.
 The `relative-path` MUST NOT start with a forward-slash character (`/`).
+The `fragment` MAY be used to identify a resource that is subordinate to the file or directory.
 
 Examples:
 
 ```plain
 bids::sub-01/fmap/sub-01_dir-AP_epi.nii.gz
 bids:ds000001:sub-02/anat/sub-02_T1w.nii.gz
 bids:myderivatives:sub-03/func/sub-03_task-rest_space-MNI152_bold.nii.gz
+bids:fmriprep:sub-001/anat/sub-001_T1w_preproc.nii.gz#aa56ztg8
+bids::prov#preprocessing-00f3a18f
 ```
 
 If no dataset name is specified, the URI is relative to the current BIDS dataset.
 This is made more precise in the next section.
 
+!!! note
+    A BIDS dataset can be referenced using the BIDS URI of its root directory.
+    For example: `bids:ds000001:.`
+
 #### Resolution of BIDS URIs
 
 In order to resolve a BIDS URI, the dataset name must be mapped to a BIDS dataset.
@@ -1054,7 +1061,7 @@ No protocol is currently proposed to automatically resolve all possible BIDS URI
 
 BIDS URIs are parsable as standard [URIs][] with scheme `bids` and path
 `[<dataset-name>]:<relative-path>`.
-The authority, query and fragment components are unused.
+The authority and query components are unused.
 Future versions of BIDS may specify interpretations for these components,
 but MUST NOT change the interpretation of a previously valid BIDS URI.
 For example, a future version may specify an authority that would allow BIDS

diff --git a/src/introduction.md b/src/introduction.md
@@ -196,6 +196,15 @@ For example:
 
 -   (publication forthcoming)
 
+### 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

diff --git a/src/metaschema.json b/src/metaschema.json
@@ -362,6 +362,15 @@
                   },
                   "additionalProperties": false
                 },
+                "modality_agnostic": {
+                  "type": "object",
+                  "patternProperties": {
+                    "^[a-zA-Z0-9_]+$": {
+                      "$ref": "#/definitions/suffixRule"
+                    }
+                  },
+                  "additionalProperties": false
+                },
                 "tables": {
                   "type": "object",
                   "patternProperties": {
@@ -375,7 +384,7 @@
                   "additionalProperties": false
                 }
               },
-              "required": ["core", "tables"],
+              "required": ["core", "modality_agnostic", "tables"],
               "additionalProperties": false
             },
             "deriv": {

diff --git a/src/modality-agnostic-files/dataset-description.md b/src/modality-agnostic-files/dataset-description.md
@@ -26,16 +26,9 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_json_table('dataset_metadata.dataset_description') }}
 
-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") }}
+!!! Note
+    See the [Provenance of a BIDS dataset](provenance.md#provenance-of-a-bids-dataset) section
+    for more information on how to describe provenance using the `GeneratedBy` field.
 
 Example: