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[ENH] BEP036 - Phenotypic Data Guidelines #2123

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3cedc86
Merge pull request #2 from bids-standard/master
ericearl May 20, 2025
11fbb47
Merge pull request #3 from bids-standard/master
ericearl May 30, 2025
0ef9fdf
[ENH] Integrate BEP036 - Phenotypic Data Guidelines
surchs May 30, 2025
0a640e6
Update phenotype.md and data-summary-files.md
ericearl May 30, 2025
a19512b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 30, 2025
5718888
Update data-summary-files.md and phenotypic-and-assessment-data.md
ericearl May 30, 2025
8f54e94
Apply suggestions from code review
ericearl May 30, 2025
94cb476
Apply suggestions from code review
ericearl May 30, 2025
142c460
Apply suggestions from code review
ericearl May 30, 2025
8b78359
Update src/modality-agnostic-files/phenotypic-and-assessment-data.md
ericearl May 30, 2025
60f712a
Update mkdocs.yml
ericearl May 30, 2025
e62b5cc
Update src/modality-agnostic-files/phenotypic-and-assessment-data.md
ericearl May 30, 2025
ac097aa
Update phenotype.md to have a macro table from schema
ericearl Jun 24, 2025
32fedd0
Update src/schema/rules/tabular_data/modality_agnostic.yaml
ericearl Jun 24, 2025
aacda9b
Update modality_agnostic.yaml
ericearl Jun 24, 2025
fd5ff2d
Update phenotype.md appendix and modality_agnostic.yaml schema
ericearl Jun 24, 2025
dd65b5e
Update modality_agnsotic.yaml
ericearl Jun 24, 2025
f4205e8
add missing column objects, use existing acq column definition (#4)
rwblair Jul 17, 2025
0eba71d
Updates for BEP036
ericearl Jul 17, 2025
d3631a8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 17, 2025
f4939ad
Updates phentoype.md and Guideline 3 in the modality agmpstic section
ericearl Jul 17, 2025
abd5c2b
Update modality_agnostic.yaml
ericearl Jul 17, 2025
ec2c53d
Update phenotypic-and-assessment_data.md
ericearl Jul 17, 2025
7639001
Merge branch 'master' into master
ericearl Jul 17, 2025
8b38859
Merge branch 'bids-standard:master' into master
ericearl Sep 15, 2025
d1141a0
Updates to remove demographics file and add AdditionalValidation field
ericearl Sep 17, 2025
6c6ee8b
Attempting to satisfy the CI and remark
ericearl Sep 17, 2025
9f8afec
Merge branch 'bids-standard:master' into master
ericearl Sep 17, 2025
8fa89bc
Update src/schema/rules/tabular_data/modality_agnostic.yaml
effigies Sep 18, 2025
ff86669
Update columns.yaml
ericearl Sep 18, 2025
ede68ef
Update modality_agnostic.yaml
ericearl Sep 18, 2025
e8ab5dd
Update phenotype.md appendix examples, participants schema, and other…
ericearl Sep 22, 2025
3490e9d
Update modality_agnostic.yaml
ericearl Sep 23, 2025
d02e0bf
Update modality_agnostic.yaml
ericearl Sep 23, 2025
f8d6333
Update modality_agnostic.yaml
ericearl Sep 23, 2025
bd083c0
Update phenotype appendix
ericearl Sep 24, 2025
ec2703b
Update phenotype appendix
ericearl Sep 24, 2025
00d8f25
Delete .vscode/settings.json
ericearl Sep 25, 2025
41f0f70
Apply suggestions from code review
ericearl Sep 25, 2025
cdfc0d2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2025
6cbb4ee
Update BEP036 files more
ericearl Sep 29, 2025
fe3ddab
Update appendices/phenotype.md
ericearl Sep 29, 2025
40f6751
Update src/schema/rules/tabular_data/modality_agnostic.yaml
ericearl Sep 30, 2025
2fd12d7
Update src/schema/objects/columns.yaml
ericearl Sep 30, 2025
a0cab8b
Update src/appendices/phenotype.md
ericearl Sep 30, 2025
c0bd78a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 30, 2025
97917f0
Update src/modality-agnostic-files/data-summary-files.md
ericearl Sep 30, 2025
80683f6
Merge branch 'master' into master
surchs Sep 30, 2025
76932fe
Move longitudinal age section to point 1
surchs Sep 30, 2025
32f994e
Revise section 5
surchs Sep 30, 2025
3a602ca
fix: Participant ID mismatch check
effigies Oct 1, 2025
f8d492e
fix(schema): Resolve a couple issues
effigies Oct 1, 2025
7f1eb09
feat: Expanded validation checks
effigies Oct 1, 2025
5c55eb9
deduplicate
effigies Oct 1, 2025
c0951f3
Promote Participants
effigies Oct 1, 2025
69183c7
feat: Make MeasurementToolMetadata recommended for phenotype files
effigies Oct 2, 2025
d3f1d0d
Updates for community review of BEP036
ericearl Oct 11, 2025
a9e2d4b
Merge branch 'master' into master
ericearl Oct 11, 2025
b60eac1
Update phenotype.md and data-summary-files.md
ericearl Nov 4, 2025
b95feec
Merge branch 'bids-standard:master' into master
ericearl Nov 4, 2025
d8b34f3
Update phenotype.md and phenotypic-and-assessment-data.md
ericearl Nov 4, 2025
b908a19
Update src/appendices/phenotype.md
ericearl Jan 21, 2026
c156df4
Catch up to the latest spec (1/21/26) (#5)
ericearl Jan 21, 2026
d2a67f6
Update modality_agnostic.yaml schema file
ericearl Jan 21, 2026
b19356f
Merge branch 'master' into master
effigies Jan 22, 2026
4be4556
Update phenotype.md and modality_agnostic.yaml
ericearl Jan 23, 2026
db34902
Merge branch 'master' into bep036-patch-mkdocs-macro
ericearl Jan 28, 2026
a7abb76
Merge remote-tracking branch 'upstream/master' into bep036-patch-mkdo…
effigies Mar 23, 2026
9dc6637
feat(schema): Add glob and zip functions to expression language
effigies Mar 6, 2026
37df2e4
feat(schema): Add dataset.{participants,sessions}_tsv to context
effigies Mar 6, 2026
878bc4a
rf(schema): Rewrite rules to use new context, glob()
effigies Mar 6, 2026
0708e30
rf(schema): Remove unused dataset.subjects from context
effigies Mar 6, 2026
4b3fdef
test(schema): Add expression tests
effigies Mar 6, 2026
46f2777
test(bst): Drop Subjects class from context types
effigies Mar 6, 2026
69c8cde
Merge remote-tracking branch 'origin/rf/tables' into bep036-patch-mkd…
effigies Mar 23, 2026
882734a
feat(schema): Add check for session_id columns
effigies Mar 17, 2026
abf16ca
feat(schema): Require aggregated session files
effigies Mar 17, 2026
2ec8859
feat(schema): Require session directories if sessions.tsv is defined
effigies Mar 17, 2026
b050199
fix: Require subject entity to trigger session entity check
effigies Mar 18, 2026
512c8d4
feat: Check for sessions.tsv file on any file with session entity
effigies Mar 18, 2026
1c9fef6
feat(metaschema): Allow for more complete issues
effigies Mar 18, 2026
ecda3ad
feat(schema): add BEP036 phenotype check rules
effigies Mar 20, 2026
4669da3
fix: Limit PhenotypeSessionAggregation to Phenotype validation
effigies Mar 23, 2026
aefcb5d
Update columns.yaml
ericearl Apr 23, 2026
d45ce4c
Update to latest BIDS spec (#7)
ericearl Jun 11, 2026
273b88e
BEP036 IndexColumns rewrite draft (#8)
ericearl Jun 18, 2026
5dce352
Update phenotype.md and longitudinal-and-multi-site-studies.md
ericearl Jun 18, 2026
12e7db1
Merge branch 'master' into bep036-patch-mkdocs-macro
ericearl Jun 18, 2026
86f8ecb
Update phenotype.md
ericearl Jun 18, 2026
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Expand Up @@ -48,6 +48,7 @@ nav:
- Quantitative MRI: appendices/qmri.md
- Arterial Spin Labeling: appendices/arterial-spin-labeling.md
- Cross modality correspondence: appendices/cross-modality-correspondence.md
- Phenotypic data guidelines: appendices/phenotype.md
- Changelog: CHANGES.md
- The BIDS Website:
- Getting started: https://bids.neuroimaging.io/getting_started/
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