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

mkdocs.yml

@@ -5,7 +5,11 @@ nav:
   - The BIDS Specification:
       - Introduction: introduction.md
       - Common principles: common-principles.md
-      - Modality agnostic files: modality-agnostic-files.md
+      - Modality agnostic files:
+          - Dataset description: modality-agnostic-files/dataset-description.md
+          - Data description: modality-agnostic-files/data-description.md
+          - Code: modality-agnostic-files/code.md
+          - Provenance: modality-agnostic-files/provenance.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
           - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
@@ -101,21 +105,15 @@ extra:
 
 extra_javascript:
   - js/jquery-3.6.0.min.js
-extra_css:
-  - css/tsv.css
 markdown_extensions:
   - toc:
       anchorlink: true
-  - attr_list
   - pymdownx.superfences:
       preserve_tabs: true
       custom_fences:
         - name: tsv
           class: tsv
           format: !!python/name:bidsschematools.render.tsv.fence
-        - name: tsvgz
-          class: tsv
-          format: !!python/name:bidsschematools.render.tsv.fence
   - admonition
   - pymdownx.details
 plugins:
@@ -132,7 +130,10 @@ plugins:
       redirect_maps:
         "01-introduction.md": "introduction.md"
         "02-common-principles.md": "common-principles.md"
-        "03-modality-agnostic-files.md": "modality-agnostic-files.md"
+        "03-modality-agnostic-files/01-dataset-description.md": "modality-agnostic-files/dataset-description.md"
+        "03-modality-agnostic-files/02-data-description.md": "modality-agnostic-files/data-description.md"
+        "03-modality-agnostic-files/03-code.md": "modality-agnostic-files/code.md"
+        "03-modality-agnostic-files/04-provenance.md": "modality-agnostic-files/provenance.md"
         "04-modality-specific-files/01-magnetic-resonance-imaging-data.md": "modality-specific-files/magnetic-resonance-imaging-data.md"
         "04-modality-specific-files/02-magnetoencephalography.md": "modality-specific-files/magnetoencephalography.md"
         "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md"

src/CHANGES.md

@@ -625,7 +625,7 @@
 ## 1.0.1-rc1
 
 -   Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file).
+-   Added support for phenotypic information split into multiple files: 3.2 Participant key file.
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.

src/appendices/meg-file-formats.md

@@ -212,7 +212,7 @@ entity to indicate each part.
 If there are multiple parts of a recording and the optional `scans.tsv` is provided,
 remember to list all files separately in `scans.tsv` and that the entries
 for the `acq_time` column in `scans.tsv` MUST all be identical, as described in
-[Scans file](../modality-agnostic-files.md#scans-file).
+[Scans file](../modality-agnostic-files/data-description.md#scans-file).
 
 Example:
 

src/appendices/qmri.md

@@ -314,7 +314,7 @@ and a guide for using macros can be found at
 ### Metadata requirements for qMRI maps
 
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
-[derived datasets](../modality-agnostic-files.md#derived-dataset-and-pipeline-description).
+[derived datasets](../modality-agnostic-files/dataset-description.md#derived-dataset-and-pipeline-description).
 
 An example `dataset_description.json` for a qMRI map derivatives directory:
 

src/common-principles.md

@@ -109,7 +109,7 @@ Data for each subject are placed in subdirectories named "`sub-<label>`",
 where string "`<label>`" is substituted with the unique identification
 label of each subject.
 Additional information on each participant MAY be provided in a
-[participants file](modality-agnostic-files.md#participants-file)
+[participants file](modality-agnostic-files/data-description.md#participants-file)
 in the root directory of the dataset.
 
 If data for the subject were acquired across multiple sessions, then within
@@ -119,7 +119,7 @@ label for each session.
 In datasets where at least one subject has more than one session, this
 additional subdirectory later SHOULD be added for all subjects in the dataset.
 Additional information on each session MAY be provided in a
-[sessions file](modality-agnostic-files.md#sessions-file)
+[sessions file](modality-agnostic-files/data-description.md#sessions-file)
 within the subject directory.
 
 Within the session subdirectory (or the subject subdirectory if no
@@ -1144,8 +1144,8 @@ to suppress warnings or provide interpretations of your filenames.
 
 <!-- Link Definitions -->
 
-[dataset-description]: modality-agnostic-files.md#dataset-description
-[dataset_description.json]: modality-agnostic-files.md#dataset_descriptionjson
-[derived-dataset-description]: modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[dataset-description]: modality-agnostic-files/data-description.md
+[dataset_description.json]: modality-agnostic-files/data-description.md#dataset_descriptionjson
+[derived-dataset-description]: modality-agnostic-files/data-description.md#derived-dataset-and-pipeline-description
 [deprecated]: #definitions
 [uris]: #uniform-resource-indicator

src/derivatives/introduction.md

@@ -129,7 +129,7 @@ for GIFTI files.
 
 [storage]: ../common-principles.md#storage-of-derived-datasets
 
-[derived-dataset-description]: ../modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[derived-dataset-description]: ../modality-agnostic-files/dataset-description.md#derived-dataset-and-pipeline-description
 
 [gifti]: https://www.nitrc.org/projects/gifti/
 

src/introduction.md

@@ -188,6 +188,12 @@ For example:
 
 -   (publication forthcoming)
 
+### Other extensions specific publications
+
+#### Provenance
+
+-   (publication forthcoming)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a

src/longitudinal-and-multi-site-studies.md

@@ -3,7 +3,7 @@
 Multiple sessions (visits) are encoded by adding an extra layer of directories
 and [filenames](common-principles.md#filenames)
 in the form of a session (for example `ses-<label>`) and
-with a [`*_sessions.tsv` file](modality-agnostic-files.md#sessions-file).
+with a [`*_sessions.tsv` file](modality-agnostic-files/data-description.md#sessions-file).
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at

src/modality-agnostic-files/code.md

@@ -0,0 +1,12 @@
+# Code
+
+Template: `code/*`
+
+Source code of scripts that were used to prepare the dataset MAY be stored here.
+Examples include deidentification or defacing of the data, or
+the conversion from the format of the source data to the BIDS format
+(see [source vs. raw vs. derived data](../common-principles.md#source-vs-raw-vs-derived-data)).
+Extra care should be taken to avoid including original IDs or
+any identifiable information with the source code.
+There are no limitations or recommendations on the language and/or
+code organization of these scripts at the moment.