Release/1.0.0#2
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Pull request overview
This PR introduces the initial (v1.0.0) GDC-style dictionary content for the repository by adding a full set of YAML-based JSON-schema-like node definitions (clinical, biospecimen, data_file, analysis workflows, etc.), along with shared _definitions, _terms, and basic repo hygiene updates.
Changes:
- Added many new node schema YAML files under
gdcdictionary/schemas/(clinical/biospecimen/data_file/analysis/etc.). - Added shared schema components (
_definitions.yaml,_terms.yaml,_settings.yaml) and schema README. - Updated
.gitignorefor common OS/test artifacts.
Reviewed changes
Copilot reviewed 59 out of 61 changed files in this pull request and generated 12 comments.
Show a summary per file
| File | Description |
|---|---|
| gdcdictionary/schemas/treatment.yaml | Adds clinical “treatment” node schema. |
| gdcdictionary/schemas/submitted_unaligned_reads.yaml | Adds data_file schema for submitted unaligned reads. |
| gdcdictionary/schemas/submitted_tangent_copy_number.yaml | Adds data_file schema for submitted tangent copy number. |
| gdcdictionary/schemas/submitted_somatic_mutation.yaml | Adds data_file schema for submitted somatic mutation. |
| gdcdictionary/schemas/submitted_methylation.yaml | Adds data_file schema for submitted methylation. |
| gdcdictionary/schemas/submitted_genotyping_array.yaml | Adds data_file schema for submitted genotyping arrays. |
| gdcdictionary/schemas/submitted_genomic_profile.yaml | Adds data_file schema for submitted genomic profiles. |
| gdcdictionary/schemas/submitted_copy_number.yaml | Adds data_file schema for submitted copy number. |
| gdcdictionary/schemas/submitted_aligned_reads.yaml | Adds data_file schema for submitted aligned reads. |
| gdcdictionary/schemas/study.yaml | Adds administrative “study” node schema. |
| gdcdictionary/schemas/structural_variation.yaml | Adds data_file schema for structural variation. |
| gdcdictionary/schemas/structural_variant_calling_workflow.yaml | Adds analysis workflow schema for SV calling. |
| gdcdictionary/schemas/somatic_copy_number_workflow.yaml | Adds analysis workflow schema for somatic copy number. |
| gdcdictionary/schemas/slide.yaml | Adds biospecimen “slide” node schema. |
| gdcdictionary/schemas/slide_image.yaml | Adds data_file schema for slide images. |
| gdcdictionary/schemas/slide_count.yaml | Adds notation schema for slide-derived counts. |
| gdcdictionary/schemas/simple_germline_variation.yaml | Adds data_file schema for simple germline variation. |
| gdcdictionary/schemas/sample.yaml | Adds biospecimen “sample” node schema. |
| gdcdictionary/schemas/rna_expression_calling_workflow.yaml | Adds analysis workflow schema for RNA expression calling. |
| gdcdictionary/schemas/README.md | Documents custom schema keywords used by the dictionary. |
| gdcdictionary/schemas/read_group.yaml | Adds biospecimen “read_group” node schema. |
| gdcdictionary/schemas/read_group_qc.yaml | Adds notation/workflow schema for read group QC. |
| gdcdictionary/schemas/publication.yaml | Adds administrative “publication” node schema. |
| gdcdictionary/schemas/projects/project1.yaml | Adds an example project-specific override schema. |
| gdcdictionary/schemas/project.yaml | Adds administrative “project” node schema. |
| gdcdictionary/schemas/program.yaml | Adds administrative “program” node schema. |
| gdcdictionary/schemas/molecular_test.yaml | Adds clinical “molecular_test” node schema. |
| gdcdictionary/schemas/mirna_expression.yaml | Adds data_file schema for miRNA expression. |
| gdcdictionary/schemas/mirna_expression_calling_workflow.yaml | Adds analysis workflow schema for miRNA expression calling. |
| gdcdictionary/schemas/lab.yaml | Adds administrative “lab” node schema. |
| gdcdictionary/schemas/keyword.yaml | Adds administrative “keyword” node schema. |
| gdcdictionary/schemas/germline_mutation_calling_workflow.yaml | Adds analysis workflow schema for germline mutation calling. |
| gdcdictionary/schemas/genomic_profile_harmonization_workflow.yaml | Adds analysis workflow schema for genomic profile harmonization. |
| gdcdictionary/schemas/gene_expression.yaml | Adds data_file schema for gene expression. |
| gdcdictionary/schemas/follow_up.yaml | Adds administrative “follow_up” node schema. |
| gdcdictionary/schemas/family_history.yaml | Adds clinical “family_history” node schema. |
| gdcdictionary/schemas/exposure.yaml | Adds clinical “exposure” node schema. |
| gdcdictionary/schemas/experimental_metadata.yaml | Adds metadata_file schema for experimental metadata. |
| gdcdictionary/schemas/experiment.yaml | Adds administrative “experiment” node schema. |
| gdcdictionary/schemas/diagnosis.yaml | Adds clinical “diagnosis” node schema. |
| gdcdictionary/schemas/demographic.yaml | Adds clinical “demographic” node schema. |
| gdcdictionary/schemas/core_metadata_collection.yaml | Adds administrative “core_metadata_collection” node schema. |
| gdcdictionary/schemas/copy_number_variation_workflow.yaml | Adds analysis workflow schema for CNV workflow. |
| gdcdictionary/schemas/copy_number_segment.yaml | Adds data_file schema for copy number segments. |
| gdcdictionary/schemas/copy_number_liftover_workflow.yaml | Adds analysis workflow schema for CN liftover. |
| gdcdictionary/schemas/copy_number_estimate.yaml | Adds data_file schema for copy number estimates. |
| gdcdictionary/schemas/copy_number_auxiliary_file.yaml | Adds data_file schema for CN pipeline auxiliary files. |
| gdcdictionary/schemas/clinical_test.yaml | Adds clinical “clinical_test” node schema. |
| gdcdictionary/schemas/case.yaml | Adds administrative “case” node schema. |
| gdcdictionary/schemas/audit.yaml | Adds administrative “audit” node schema. |
| gdcdictionary/schemas/aliquot.yaml | Adds biospecimen “aliquot” node schema. |
| gdcdictionary/schemas/alignment_workflow.yaml | Adds analysis workflow schema for alignments. |
| gdcdictionary/schemas/alignment_cocleaning_workflow.yaml | Adds analysis workflow schema for alignment+cocleaning. |
| gdcdictionary/schemas/aligned_reads.yaml | Adds data_file schema for aligned reads. |
| gdcdictionary/schemas/aligned_reads_index.yaml | Adds index_file schema for aligned reads indexes. |
| gdcdictionary/schemas/acknowledgement.yaml | Adds administrative “acknowledgement” node schema. |
| gdcdictionary/schemas/_settings.yaml | Adds dictionary settings metadata. |
| gdcdictionary/schemas/_definitions.yaml | Adds shared schema definitions used across node schemas. |
| .gitignore | Ignores OS and test result artifacts. |
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| type: | ||
| enum: | ||
| - aligned_reads |
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| properties: | ||
| project_1_specific_thing: | ||
| type: string |
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| type: | ||
| enum: | ||
| - germline_mutation_calling_workflow |
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| workflow_type: | ||
| term: | ||
| $ref: _terms.yaml#/workflow_type | ||
| enum: | ||
| - HaplotypeCaller |
| # - 'No' | ||
| # - N/A | ||
| sample_exception_hemolyzed: | ||
| desciption: Text term that represents if the sample exception was applied due |
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| enum: | ||
| - BAI | ||
| - CRAI | ||
| - CRAM |
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| - type: array | ||
| items: | ||
| $ref: '#/foreign_key_project' | ||
| minItems: 1 | ||
| maxItems: 1 | ||
| - $ref: '#/foreign_key_project' |
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| - type: array | ||
| items: | ||
| $ref: '#/foreign_key_project' | ||
| minItems: 1 | ||
| - $ref: '#/foreign_key_project' |
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| - type: array | ||
| items: | ||
| $ref: '#/foreign_key' | ||
| minItems: 1 | ||
| maxItems: 1 | ||
| - $ref: '#/foreign_key' |
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| - type: array | ||
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| - $ref: '#/foreign_key' |
Bearbbcjtc
approved these changes
Jun 23, 2026
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Initial version of IPO dictionary created and deployed in February 2025.