diff --git a/gdcdictionary/schemas/aligned_reads_file.yaml b/gdcdictionary/schemas/aligned_reads_file.yaml index 9f98bd1..79a2c4a 100644 --- a/gdcdictionary/schemas/aligned_reads_file.yaml +++ b/gdcdictionary/schemas/aligned_reads_file.yaml @@ -104,6 +104,12 @@ properties: # - Amplicon # - Other + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + read_groups: $ref: "_definitions.yaml#/to_many" core_metadata_collections: diff --git a/gdcdictionary/schemas/aligned_reads_index_file.yaml b/gdcdictionary/schemas/aligned_reads_index_file.yaml index 3adafd6..d88287c 100644 --- a/gdcdictionary/schemas/aligned_reads_index_file.yaml +++ b/gdcdictionary/schemas/aligned_reads_index_file.yaml @@ -50,25 +50,23 @@ properties: term: $ref: "_terms.yaml#/data_category" type: string - # enum: - # - Sequencing Data - # - Sequencing Reads - # - Raw Sequencing Data data_type: term: $ref: "_terms.yaml#/data_type" type: string - # enum: [ "Aligned Reads Index" ] data_format: term: $ref: "_terms.yaml#/data_format" type: string - # enum: - # - BAI - # - CRAI + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + aligned_reads_files: $ref: "_definitions.yaml#/to_one" core_metadata_collections: diff --git a/gdcdictionary/schemas/annotation.yaml b/gdcdictionary/schemas/annotation.yaml index 3252581..4670692 100644 --- a/gdcdictionary/schemas/annotation.yaml +++ b/gdcdictionary/schemas/annotation.yaml @@ -122,6 +122,12 @@ properties: maximum: 24 minimum: 0 + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + sift_image_quality_index: description: A score of image quality based on the SIFT annotation software. enum: diff --git a/gdcdictionary/schemas/clinical_file.yaml b/gdcdictionary/schemas/clinical_file.yaml index bdc3852..8fd326e 100644 --- a/gdcdictionary/schemas/clinical_file.yaml +++ b/gdcdictionary/schemas/clinical_file.yaml @@ -77,6 +77,12 @@ properties: description: "The text term describing the file format of the supplementary file, for example, PDF, XLSX, JPEG, PNG, TSV, etc." type: string + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + core_metadata_collections: description: The submitter_id or id of the core_metadata_collection to which the supplementary file belongs, i.e., a link to a record in the parent node. $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/image_file.yaml b/gdcdictionary/schemas/image_file.yaml index f4e07ce..4915b0e 100644 --- a/gdcdictionary/schemas/image_file.yaml +++ b/gdcdictionary/schemas/image_file.yaml @@ -92,6 +92,12 @@ properties: - "Poor image quality" - "Not Reported" + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + series_instance_uid: description: > Formal identifier for this image or other content. diff --git a/gdcdictionary/schemas/unaligned_reads_file.yaml b/gdcdictionary/schemas/unaligned_reads_file.yaml index 83011d8..d90d415 100644 --- a/gdcdictionary/schemas/unaligned_reads_file.yaml +++ b/gdcdictionary/schemas/unaligned_reads_file.yaml @@ -69,6 +69,12 @@ properties: $ref: "_terms.yaml#/experimental_strategy" type: string + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + read_groups: $ref: "_definitions.yaml#/to_many" core_metadata_collections: diff --git a/gdcdictionary/schemas/variant_call_file.yaml b/gdcdictionary/schemas/variant_call_file.yaml index cc1b776..157c655 100644 --- a/gdcdictionary/schemas/variant_call_file.yaml +++ b/gdcdictionary/schemas/variant_call_file.yaml @@ -76,6 +76,12 @@ properties: $ref: "_terms.yaml#/experimental_strategy" type: string + object_ids: + description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable. + type: array + items: + type: string + variant_calling_workflow_type: # from BDC germline_mutation_calling_workflow node description: The workflow used to call germline mutations from sequencing reads, e.g., HaplotypeCaller. type: string