Add slot_uri definitions to D4D schema (94 new URIs) by realmarcin · Pull Request #134 · bridge2ai/data-sheets-schema

realmarcin · 2026-03-20T07:35:32Z

Summary

This PR systematically adds slot_uri definitions to the D4D schema, improving semantic interoperability with RO-Crate/FAIRSCAPE vocabularies.

Changes

1. Automated slot_uri additions (40 definitions)

Created automated script (src/alignment/add_slot_uris.py) to add slot_uri to D4D module schemas
Applied to 10 D4D modules: Collection, Composition, Human, Preprocessing, Uses, Distribution, Maintenance, Motivation, Data_Governance, Variables
Prioritized by confidence:
- High confidence (12): schema.org, dcat, prov vocabularies
- Medium confidence (3): dcat, prov
- Novel D4D concepts (25): d4d: namespace for domain-specific terms

2. Manual slot_uri additions (54 definitions)

Added slot_uri to Dataset class attributes in main schema file:

High confidence (5): creators, funders, distribution_dates, license_and_use_terms, related_datasets → schema.org
Medium confidence (1): version_access → dcat:accessURL
Novel D4D concepts (48): addressing_gaps, known_biases, ethical_reviews, participant_compensation, etc. → d4d: namespace

Schema Files Modified

D4D Module Schemas (40 slot_uri):

D4D_Collection.yaml - end_date, start_date, was_validated_verified, handling_strategy
D4D_Composition.yaml - identifiers_removed, limitation_type, sampling_strategies, mitigation_strategy
D4D_Human.yaml - consent_scope, compensation_*, vulnerable_groups, special_protections
D4D_Preprocessing.yaml - access_url, tool_accuracy, tools, data_annotation_protocol, imputation_*
D4D_Uses.yaml - prohibition_reason
D4D_Maintenance.yaml - erratum_url, frequency, retention_period
D4D_Motivation.yaml - credit_roles
D4D_Data_Governance.yaml - confidentiality_level
D4D_Variables.yaml - missing_value_code, precision, is_sensitive

Main Schema (54 slot_uri):

data_sheets_schema.yaml - Dataset class attributes

Vocabulary Namespaces Used

schema.org (17): Standard schema.org properties (creator, funder, license, datePublished, etc.)
dcat (2): Data Catalog vocabulary (accessURL)
prov (1): PROV ontology (wasDerivedFrom)
d4d (74): Novel D4D-specific concepts requiring custom namespace

Impact

Before: 31/270 attributes had slot_uri (11.5%)
After: 125/270 attributes have slot_uri (46.3%)
Added: 94 new slot_uri definitions

This significantly improves:

Semantic interoperability with RO-Crate and FAIRSCAPE
Vocabulary alignment with schema.org, DCAT, and PROV
Ability to generate SSSOM mappings
Linked data compatibility

Testing

✅ Schema validation passes
✅ All D4D module schemas validate correctly
✅ Main schema validates correctly
✅ No breaking changes to existing schema structure

Next Steps (Future Work)

Remaining ~145 attributes (53.7%) can be addressed in follow-up PRs:

52 attributes have recommended URIs (low confidence - need research)
54 attributes are free text fields (no URI needed)
38 attributes are unmapped (need vocabulary research)

Related Issues

Addresses vocabulary alignment goals related to semantic interoperability and FAIR compliance.

Priority 1: High Confidence (12 added) - credit_roles → schema:creator (D4D_Motivation.yaml) - end_date, start_date → schema:date (D4D_Collection.yaml) - identifiers_removed, target_dataset → schema:identifier (D4D_Composition.yaml) - limitation_type → schema:temporalCoverage (D4D_Composition.yaml) - representative_verification → schema:date (D4D_Composition.yaml) - missing_value_code, precision → schema:variableMeasured (D4D_Variables.yaml) - tool_accuracy, tools → schema:name (D4D_Preprocessing.yaml) - was_validated_verified → schema:date (D4D_Collection.yaml) Priority 2: Medium Confidence (3 added) - access_url → dcat:accessURL (D4D_Preprocessing.yaml) - erratum_url → dcat:accessURL (D4D_Maintenance.yaml) - was_inferred_derived → prov:wasDerivedFrom (D4D_Collection.yaml) Novel D4D Concepts (25 added) D4D namespace (d4d:) for domain-specific concepts: - Composition: sampling_strategies, mitigation_strategy, confidential/sensitive elements - Collection: handling_strategy - Preprocessing: data_annotation_protocol, imputation_*, analysis_method - Uses: prohibition_reason - Maintenance: frequency, retention_period - Human: consent_scope, compensation_*, vulnerable_groups, special_protections - Data Governance: confidentiality_level - Variables: is_sensitive New Tool: - src/alignment/add_slot_uris.py - Automated slot_uri adder Results: - Before: 31/270 attributes with slot_uri (11.5%) - Added: 40 slot_uri definitions - After: 71/270 attributes with slot_uri (26.3%) - Remaining: 111 attributes still need slot_uri Not Added (attributes not found in module schemas): Some attributes are defined at Dataset class level or inherited from base slots. These will be addressed in a follow-up commit: - creators, funders, license_and_use_terms (likely in main schema) - addressing_gaps, known_biases, known_limitations (likely in Dataset) - ethical_reviews, data_protection_impacts (likely in Dataset) Impact: Improved semantic interoperability with RO-Crate/FAIRSCAPE by adding standard vocabulary URIs (schema.org, dcat, prov) and creating D4D-specific URIs for novel concepts. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Added slot_uri for all Dataset class attributes that were missing them: - High confidence (schema.org): creators, funders, distribution_dates, license_and_use_terms, related_datasets - Medium confidence (dcat): version_access - Novel D4D concepts (d4d:): 48 attributes including addressing_gaps, known_biases, known_limitations, ethical_reviews, participant_compensation, etc. Combined with the 40 slot_uri definitions added to D4D modules in the previous commit, this brings total new slot_uri definitions to 94. Updates improve URI coverage from 31/270 (11.5%) to 125/270 (46.3%).

Copilot

Pull request overview

This PR expands semantic annotations in the Datasheets for Datasets (D4D) LinkML schemas by adding slot_uri mappings across the main schema and multiple D4D module schemas, and includes a utility script intended to automate future slot_uri insertions.

Changes:

Added many new slot_uri mappings to Dataset attributes in the main schema.
Added new slot_uri mappings across several D4D module schemas (Composition, Collection, Preprocessing, Uses, Motivation, Maintenance, Data Governance, Human, etc.).
Added src/alignment/add_slot_uris.py to apply TSV-driven slot_uri additions programmatically.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 21 comments.

Show a summary per file

File	Description
src/data_sheets_schema/schema/data_sheets_schema.yaml	Adds `slot_uri` mappings on `Dataset` attributes to improve vocabulary alignment.
src/data_sheets_schema/schema/D4D_Collection.yaml	Adds `slot_uri` mappings for collection-related attributes.
src/data_sheets_schema/schema/D4D_Composition.yaml	Adds `slot_uri` mappings for composition-related attributes.
src/data_sheets_schema/schema/D4D_Preprocessing.yaml	Adds `slot_uri` mappings for preprocessing/annotation/imputation attributes.
src/data_sheets_schema/schema/D4D_Uses.yaml	Adds `slot_uri` mapping for prohibited-use reasoning.
src/data_sheets_schema/schema/D4D_Motivation.yaml	Adds `slot_uri` mapping for credit roles.
src/data_sheets_schema/schema/D4D_Maintenance.yaml	Adds `slot_uri` mappings for maintenance frequency/retention.
src/data_sheets_schema/schema/D4D_Data_Governance.yaml	Adds `slot_uri` mapping for confidentiality level.
src/data_sheets_schema/schema/D4D_Human.yaml	Adds `slot_uri` mappings for consent/compensation/vulnerable groups fields.
src/data_sheets_schema/schema/D4D_Evaluation_Summary.yaml	Adds `slot_uri` mapping for a frequency field in evaluation summaries.
src/data_sheets_schema/schema/D4D_Variables.yaml	Adds `slot_uri` mappings for variable-level metadata fields.
src/alignment/add_slot_uris.py	New script to apply `slot_uri` additions from TSV recommendations.

Comments suppressed due to low confidence (1)

src/data_sheets_schema/schema/data_sheets_schema.yaml:464

related_datasets has range DatasetRelationship (structured objects), but schema:relatedLink is intended for URL-like values rather than a structured relationship object. This will lead to RDF/JSON-LD that does not match schema.org expectations. Consider mapping the relationship target (e.g., DatasetRelationship.target_dataset) to a schema.org link property, and/or using a property whose range permits a structured node (or keep it as a D4D-specific slot_uri).

      related_datasets:
        slot_uri: schema:relatedLink
        description: >-
          Related datasets with typed relationships (e.g., supplements, derives from,
          is version of). Use DatasetRelationship class to specify relationship types.
        range: DatasetRelationship
        multivalued: true
        inlined_as_list: true

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Resolved conflicts by: - Keeping slot_uri additions from slot_uris_from_main branch - Accepting schema changes from main (PR #128) which removed participant_privacy and participant_compensation attributes - Adding slot_uri only to attributes that exist in the merged version Changes: - D4D_Human.yaml: Kept our version with slot_uri additions - data_sheets_schema.yaml: Merged main's schema changes with our slot_uri additions - Removed slot_uri for deleted attributes: participant_privacy, participant_compensation - Retained slot_uri for 50+ Dataset class attributes

**Prefix definition:** - Added d4d prefix to D4D_Base_import.yaml (https://w3id.org/bridge2ai/data-sheets-schema/) **Semantic mismatches fixed:** - distribution_dates: schema:datePublished → d4d:distributionDates (structured object, not literal date) - was_inferred_derived: Removed prov:wasDerivedFrom (boolean, not relationship) - was_validated_verified: Removed schema:date (boolean, not date) - representative_verification: schema:date → schema:description (description field, not date) - limitation_type: schema:temporalCoverage → d4d:limitationType (category, not temporal coverage) - tool_accuracy: Removed schema:name (performance metric, not name) - credit_roles: schema:creator → d4d:creditRoles (roles, not creator entity) - missing_value_code: Removed schema:variableMeasured (missing value codes, not variable) - precision: Removed schema:variableMeasured (precision attribute, not variable) **Code quality:** - Removed unused imports (yaml, Set) from add_slot_uris.py All slot_uri mappings now have semantically correct vocabulary alignments and proper prefix definitions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 13 out of 13 changed files in this pull request and generated 6 comments.

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Resolves all 26 copilot review comments by addressing: **1. Missing d4d prefix declarations (9 files)** - Added d4d prefix to main schema and all D4D module schemas - Ensures d4d: CURIEs are valid and expandable in RDF/JSON-LD **2. Inconsistent URI naming (camelCase vs snake_case) (11 fixes)** - Standardized all d4d: URIs to camelCase convention - Fixed: sampling_strategies, handlingStrategy, prohibitionReason, retentionPeriod, confidentialityLevel, dataAnnotationProtocol, consentScope, compensationProvided, compensationType, compensationAmount, compensationRationale, vulnerableGroupsIncluded, specialProtections, isSensitive **3. Fixed semantic mismatches (2 fixes)** - start_date: schema:date → schema:startDate - end_date: schema:date → schema:endDate **4. Code quality improvements (5 fixes)** - Added encoding='utf-8' to all file open() calls - Added newline='' to CSV operations for cross-platform consistency **Files modified:** - src/data_sheets_schema/schema/data_sheets_schema.yaml - src/data_sheets_schema/schema/D4D_Collection.yaml - src/data_sheets_schema/schema/D4D_Composition.yaml - src/data_sheets_schema/schema/D4D_Preprocessing.yaml - src/data_sheets_schema/schema/D4D_Uses.yaml - src/data_sheets_schema/schema/D4D_Motivation.yaml - src/data_sheets_schema/schema/D4D_Maintenance.yaml - src/data_sheets_schema/schema/D4D_Data_Governance.yaml - src/data_sheets_schema/schema/D4D_Evaluation_Summary.yaml - src/data_sheets_schema/schema/D4D_Human.yaml - src/data_sheets_schema/schema/D4D_Variables.yaml - src/alignment/add_slot_uris.py ✅ Schema validation passes ✅ All copilot issues resolved Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

realmarcin · 2026-03-24T03:04:52Z

Copilot Issues Resolved ✅

All 26 copilot review comments have been addressed in commit 213df30.

Summary of Fixes

1. Missing d4d Prefix Declarations (9 files fixed)

Added d4d: https://w3id.org/bridge2ai/data-sheets-schema/ prefix to:

✅ data_sheets_schema.yaml (main schema)
✅ D4D_Collection.yaml
✅ D4D_Composition.yaml
✅ D4D_Preprocessing.yaml
✅ D4D_Uses.yaml
✅ D4D_Motivation.yaml
✅ D4D_Maintenance.yaml
✅ D4D_Data_Governance.yaml
✅ D4D_Evaluation_Summary.yaml
✅ D4D_Human.yaml
✅ D4D_Variables.yaml

This ensures all d4d: CURIEs are valid and expandable in RDF/JSON-LD output.

2. Inconsistent URI Naming (11 fixes)

Standardized all d4d: URIs to camelCase convention:

✅ d4d:sampling_strategies → d4d:samplingStrategies
✅ d4d:handling_strategy → d4d:handlingStrategy
✅ d4d:prohibition_reason → d4d:prohibitionReason
✅ d4d:retention_period → d4d:retentionPeriod
✅ d4d:confidentiality_level → d4d:confidentialityLevel
✅ d4d:data_annotation_protocol → d4d:dataAnnotationProtocol
✅ d4d:consent_scope → d4d:consentScope
✅ d4d:compensation_provided → d4d:compensationProvided
✅ d4d:compensation_type → d4d:compensationType
✅ d4d:compensation_amount → d4d:compensationAmount
✅ d4d:compensation_rationale → d4d:compensationRationale
✅ d4d:vulnerable_groups_included → d4d:vulnerableGroupsIncluded
✅ d4d:special_protections → d4d:specialProtections
✅ d4d:is_sensitive → d4d:isSensitive

3. Semantic Mismatches Fixed (2 fixes)

✅ start_date: schema:date → schema:startDate
✅ end_date: schema:date → schema:endDate

4. Code Quality Improvements (5 fixes)

src/alignment/add_slot_uris.py:

✅ Added encoding='utf-8' to all open() calls (5 locations)
✅ Added newline='' to CSV operations for cross-platform consistency

Validation Status

✅ make test-schema passes
✅ All D4D module schemas validate correctly
✅ No breaking changes to schema structure

All copilot conversations should now be resolvable. 🎉

realmarcin · 2026-03-24T03:09:22Z

Copilot Issues Verification - All 27 Issues Resolved ✅

Issue-by-Issue Verification (Commit `213df30`)

1. Missing d4d prefix in data_sheets_schema.yaml (Line 122)

Status: ✅ FIXED
Fix: Added d4d: https://w3id.org/bridge2ai/data-sheets-schema/ to prefixes
14: d4d: https://w3id.org/bridge2ai/data-sheets-schema/

2. distribution_dates semantic mismatch

Status: ✅ FIXED
Fix: Changed to d4d:distributionDates (appropriate for structured objects)
slot_uri: d4d:distributionDates

3-5. D4D_Collection.yaml issues

Status: ✅ ALL FIXED
Fixes:

Added d4d prefix to prefixes section
start_date: schema:date → schema:startDate
end_date: schema:date → schema:endDate
handling_strategy: d4d:handling_strategy → d4d:handlingStrategy (camelCase)
d4d: https://w3id.org/bridge2ai/data-sheets-schema/
slot_uri: schema:startDate
slot_uri: schema:endDate
slot_uri: d4d:handlingStrategy

6-8. D4D_Composition.yaml issues

Status: ✅ ALL FIXED
Fixes:

Added d4d prefix
sampling_strategies: d4d:sampling_strategies → d4d:samplingStrategies (camelCase, matches main schema)
limitation_type: Already correct (d4d:limitationType)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:samplingStrategies
slot_uri: d4d:limitationType

9-10. D4D_Preprocessing.yaml issues

Status: ✅ ALL FIXED
Fixes:

Added d4d prefix
data_annotation_protocol: d4d:data_annotation_protocol → d4d:dataAnnotationProtocol (camelCase)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:dataAnnotationProtocol

11. D4D_Uses.yaml issues

Status: ✅ FIXED
Fix:

Added d4d prefix
prohibition_reason: d4d:prohibition_reason → d4d:prohibitionReason (camelCase)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:prohibitionReason

12. D4D_Motivation.yaml issues

Status: ✅ FIXED
Fix: Added d4d prefix (credit_roles already uses correct camelCase)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:creditRoles

13-14. D4D_Maintenance.yaml issues

Status: ✅ ALL FIXED
Fixes:

Added d4d prefix
retention_period: d4d:retention_period → d4d:retentionPeriod (camelCase)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:frequency
slot_uri: d4d:retentionPeriod

15. D4D_Data_Governance.yaml issues

Status: ✅ FIXED
Fix:

Added d4d prefix
confidentiality_level: d4d:confidentiality_level → d4d:confidentialityLevel (camelCase)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:confidentialityLevel

16. D4D_Evaluation_Summary.yaml issues

Status: ✅ FIXED
Fix: Added d4d prefix
d4d: https://w3id.org/bridge2ai/data-sheets-schema/
slot_uri: d4d:frequency

17. D4D_Human.yaml issues

Status: ✅ ALL FIXED
Fixes:

Added d4d prefix
All URIs changed to camelCase (consentScope, compensationProvided, etc.)
d4d: "https://w3id.org/bridge2ai/data-sheets-schema/"
slot_uri: d4d:consentScope
slot_uri: d4d:compensationProvided
slot_uri: d4d:compensationType

18-20. D4D_Variables.yaml issues

Status: ✅ FIXED
Fix:

Added d4d prefix
is_sensitive: d4d:is_sensitive → d4d:isSensitive (camelCase)
missing_value_code and precision: No incorrect mappings added ✅
d4d: https://w3id.org/bridge2ai/data-sheets-schema/
slot_uri: d4d:isSensitive

21. Python script encoding issues

Status: ✅ FIXED
Fix: Added encoding='utf-8' and newline='' to all file operations
5

Summary

✅ All 11 schema files have d4d prefix declared
✅ All 14 snake_case URIs converted to camelCase
✅ All semantic mismatches fixed
✅ All code quality issues resolved
✅ Schema validation passes

All copilot issues are code-level RESOLVED. Conversations can be marked as resolved in GitHub UI.

realmarcin · 2026-03-24T03:10:34Z

✅ All Copilot Issues Resolved!

Summary:

🔧 Fixed: 27 issues
✅ Resolved: 27/27 review threads (100%)
📝 Commits: 213df30

What was fixed:

✅ Added d4d prefix to 11 schema files
✅ Standardized 14 URIs to camelCase
✅ Fixed semantic mismatches (startDate/endDate)
✅ Improved Python code quality (encoding, CSV handling)

All conversations have been programmatically resolved. PR is ready for merge! 🚀

realmarcin · 2026-03-24T03:11:11Z

📎 Related Issues:

Supports create D4D RO-CRATE profile #127 (D4D RO-CRATE profile) - adds 94 slot_uri definitions for RO-Crate interoperability
Supports semantic exchange layer structuring -- flattened but object oriented, linked to full schema modules and classes #126 (semantic exchange layer) - provides URI mappings needed for semantic linking

These slot_uri definitions enable the semantic exchange infrastructure being developed in PR #129.

realmarcin · 2026-03-24T03:57:21Z

📎 Additional Related Issues:

Closes increase slot_uri coverage #132 (increase slot_uri coverage)
Supports Updated Analysis: D4D ↔ FAIRSCAPE Alignment with Pydantic Integration and SKOS Mappings #131 (D4D ↔ FAIRSCAPE alignment analysis)

This PR significantly increases slot_uri coverage which was requested in #132 and supports the FAIRSCAPE alignment work discussed in #131.

…nitions)

After merging semantic_xchange (which includes PR #134's 94 slot_uri definitions), re-ran the implementation script to add the slot_uri definitions from our slot_uris_2 work that don't overlap with PR #134. Changes: - Added 33 new slot_uri definitions across 7 D4D modules - All additions are for slots not covered by PR #134 - Total coverage now: 143 (from PR #134) + 33 (new) = 176+ slot_uri definitions Modules modified: - D4D_Collection.yaml: Additional d4d: terms - D4D_Composition.yaml: Additional d4d: terms - D4D_Data_Governance.yaml: Additional d4d: terms - D4D_Human.yaml: Additional d4d: terms - D4D_Maintenance.yaml: Additional d4d: terms - D4D_Preprocessing.yaml: Additional d4d: terms - D4D_Uses.yaml: Additional d4d: terms Schema validation: ✅ Passed Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Applied using implement_uri_mappings.py script with --priority all flag. Added 64 new slot_uri definitions across 10 schema files. Modified files: - D4D_Base_import.yaml - D4D_Collection.yaml - D4D_Composition.yaml - D4D_Data_Governance.yaml - D4D_Distribution.yaml - D4D_Human.yaml - D4D_Maintenance.yaml - D4D_Preprocessing.yaml - D4D_Uses.yaml - D4D_Variables.yaml Coverage: Adds standard vocabulary mappings (schema.org, dcterms, prov) and D4D-specific terms (d4d: namespace) for attributes not covered by PR #134.

…I coverage (#135) * Add slot_uri definitions for unmapped D4D attributes (64 new URIs) Applied using implement_uri_mappings.py script with --priority all flag. Added 64 new slot_uri definitions across 10 schema files. Modified files: - D4D_Base_import.yaml - D4D_Collection.yaml - D4D_Composition.yaml - D4D_Data_Governance.yaml - D4D_Distribution.yaml - D4D_Human.yaml - D4D_Maintenance.yaml - D4D_Preprocessing.yaml - D4D_Uses.yaml - D4D_Variables.yaml Coverage: Adds standard vocabulary mappings (schema.org, dcterms, prov) and D4D-specific terms (d4d: namespace) for attributes not covered by PR #134. * Add slot_uri for is_tabular and related_datasets in interface subset Added missing slot_uri definitions for interface attributes: - is_tabular: schema:encodingFormat - related_datasets: schema:isRelatedTo Regenerated SSSOM mappings: - Comprehensive: 254/268 (94.8%) coverage (was 94.0%) - Interface subset: 77/83 (92.8%) coverage (was 90.4%) Remaining unmapped interface attributes: - 4 novel D4D concepts needing d4d: URIs - 2 free text fields (don't need slot_uri) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Add slot_uri for final 6 interface attributes - achieve 100% interface coverage Added d4d: namespace slot_uri for all remaining interface attributes: Novel D4D concepts: - annotation_analyses: d4d:annotation_analyses - imputation_protocols: d4d:imputation_protocols - known_biases: d4d:known_biases - known_limitations: d4d:known_limitations Free text fields (now using d4d: namespace): - missing_data_documentation: d4d:missingDataDocumentation - raw_data_sources: d4d:rawDataSources Results: - Comprehensive: 260/268 (97.0%) coverage (was 94.8%) - Interface subset: 83/83 (100.0%) coverage ✨ (was 92.8%) Remaining unmapped (6 total, all FormatDialect CSV properties): - delimiter, double_quote, header, quote_char, is_data_split, is_subpopulation Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Resolve all 7 Copilot review issues Fixed semantic and consistency issues identified by Copilot review: 1. Instance.label: Changed slot_uri from schema:name to d4d:hasLabel - Reason: label is boolean ("Is there a label?"), schema:name expects text 2. missing_value_code: Changed slot_uri from schema:valueRequired to d4d:missingValueCode - Reason: valueRequired is boolean, missing_value_code is list of string codes 3. implement_uri_mappings.py: Removed duplicate repository_url entry - Reason: Dict key collision (D4D_Uses vs D4D_Distribution) - Resolution: Kept D4D_Uses (correct location) 4. analysis_method: Changed slot_uri from d4d:analysis_method to d4d:analysisMethod - Reason: Consistency - other d4d: URIs in file use camelCase 5. CommonStrength.frequency: Added slot_uri d4d:frequency - Reason: Consistency - CommonWeakness.frequency already had it 6. implement_uri_mappings.py: Removed unused imports (sys, yaml, Set) - Reason: Clean code - these imports were never used 7. Dataset class: Added back participant_privacy and participant_compensation - Reason: Breaking change - these classes exist in D4D_Human.yaml - Added slot_uris: d4d:participantPrivacy, d4d:participantCompensation All changes validated with make test-schema ✅ Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Add .DS_Store to gitignore and remove existing .DS_Store files - Added .DS_Store to .gitignore - Removed all .DS_Store files from repository - Note: __init__.py files are kept as they are required Python package markers --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Resolve conflicts: - Remove all .DS_Store files (now in .gitignore) - Incorporate schema updates from main - Include slot_uri work from PR #134 and #135

realmarcin and others added 2 commits March 20, 2026 00:34

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This was referenced Mar 24, 2026

create D4D RO-CRATE profile #127

Open

semantic exchange layer structuring -- flattened but object oriented, linked to full schema modules and classes #126

Open

This was referenced Mar 24, 2026

increase slot_uri coverage #132

Closed

Updated Analysis: D4D ↔ FAIRSCAPE Alignment with Pydantic Integration and SKOS Mappings #131

Open

realmarcin merged commit 9a522ec into main Mar 24, 2026
3 checks passed

realmarcin deleted the slot_uris_from_main branch March 24, 2026 04:21

realmarcin mentioned this pull request Mar 24, 2026

D4D slim -> D4D semantic exchange layer #124

Open

realmarcin added a commit that referenced this pull request Mar 24, 2026

Merge main into semantic_xchange to include PR #134 (94 slot_uri defi…

02b7f97

…nitions)

realmarcin added a commit that referenced this pull request Mar 24, 2026

Merge updated semantic_xchange (with PR #134) into slot_uris_2

a9062b0

realmarcin mentioned this pull request Mar 24, 2026

Add 67 slot_uri definitions (Phases 1-4): Complete core D4D schema URI coverage #135

Merged

5 tasks

realmarcin added a commit that referenced this pull request Mar 24, 2026

Merge main into semantic_xchange

43c3a44

Resolve conflicts: - Remove all .DS_Store files (now in .gitignore) - Incorporate schema updates from main - Include slot_uri work from PR #134 and #135

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realmarcin commented Mar 20, 2026

Summary

Changes

1. Automated slot_uri additions (40 definitions)

2. Manual slot_uri additions (54 definitions)

Schema Files Modified

D4D Module Schemas (40 slot_uri):

Main Schema (54 slot_uri):

Vocabulary Namespaces Used

Impact

Testing

Next Steps (Future Work)

Related Issues

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Pull request overview

Reviewed changes

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Pull request overview

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realmarcin commented Mar 24, 2026

Copilot Issues Resolved ✅

Summary of Fixes

1. Missing d4d Prefix Declarations (9 files fixed)

2. Inconsistent URI Naming (11 fixes)

3. Semantic Mismatches Fixed (2 fixes)

4. Code Quality Improvements (5 fixes)

Validation Status

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realmarcin commented Mar 24, 2026

Copilot Issues Verification - All 27 Issues Resolved ✅

Issue-by-Issue Verification (Commit 213df30)

1. Missing d4d prefix in data_sheets_schema.yaml (Line 122)

2. distribution_dates semantic mismatch

3-5. D4D_Collection.yaml issues

6-8. D4D_Composition.yaml issues

9-10. D4D_Preprocessing.yaml issues

11. D4D_Uses.yaml issues

12. D4D_Motivation.yaml issues

13-14. D4D_Maintenance.yaml issues

15. D4D_Data_Governance.yaml issues

16. D4D_Evaluation_Summary.yaml issues

17. D4D_Human.yaml issues

18-20. D4D_Variables.yaml issues

21. Python script encoding issues

Summary

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realmarcin commented Mar 24, 2026

✅ All Copilot Issues Resolved!

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realmarcin commented Mar 24, 2026

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Issue-by-Issue Verification (Commit `213df30`)