diff --git a/gdcdictionary/schemas/reference_file.yaml b/gdcdictionary/schemas/reference_file.yaml index 82f9653..6087a6f 100644 --- a/gdcdictionary/schemas/reference_file.yaml +++ b/gdcdictionary/schemas/reference_file.yaml @@ -87,6 +87,7 @@ properties: - ALT - AMB - ANN + - ARR - AVRO - BCF - BED diff --git a/gdcdictionary/schemas/submitted_expression_array.yaml b/gdcdictionary/schemas/submitted_expression_array.yaml new file mode 100644 index 0000000..24ee685 --- /dev/null +++ b/gdcdictionary/schemas/submitted_expression_array.yaml @@ -0,0 +1,95 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "submitted_expression_array" +title: Submitted Expression Array +type: object +namespace: https://dcp.bionimbus.org/ +category: data_file +program: '*' +project: '*' +description: > + Data file containing raw data from an expression array. +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - created_datetime + - updated_datetime + - state + - file_state + - error_type + +links: + - exclusive: false + required: true + subgroup: + - name: core_metadata_collections + backref: submitted_expression_arrays + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false + - name: aliquots + backref: submitted_expression_arrays + label: derived_from + target_type: aliquot + multiplicity: many_to_one + required: false + +required: + - type + - submitter_id + - file_name + - file_size + - md5sum + - data_category + - data_type + - data_format + - experimental_strategy + - platform + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + $ref: "_definitions.yaml#/data_file_properties" + + data_category: + term: + $ref: "_terms.yaml#/data_category" + enum: + - Transcriptome Profiling + + data_format: + term: + $ref: "_terms.yaml#/data_format" + enum: + - CEL + + data_type: + term: + $ref: "_terms.yaml#/data_type" + enum: + - Raw Intensities + + experimental_strategy: + term: + $ref: "_terms.yaml#/experimental_strategy" + enum: + - Expression Array + + platform: + term: + $ref: "_terms.yaml#/platform" + enum: + - GeneChip U133 Plus 2.0 + - GeneChip U133A + + aliquots: + $ref: "_definitions.yaml#/to_one" + core_metadata_collections: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_genotyping_array.yaml b/gdcdictionary/schemas/submitted_genotyping_array.yaml new file mode 100644 index 0000000..5c62d05 --- /dev/null +++ b/gdcdictionary/schemas/submitted_genotyping_array.yaml @@ -0,0 +1,91 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "submitted_genotyping_array" +title: Submitted Genotyping Array +type: object +namespace: https://dcp.bionimbus.org/ +category: data_file +program: '*' +project: '*' +description: > + Data file containing raw data from a genotyping array. +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - created_datetime + - updated_datetime + - state + - file_state + - error_type + +links: + - exclusive: false + required: true + subgroup: + - name: core_metadata_collections + backref: submitted_genotyping_arrays + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false + - name: aliquots + backref: submitted_genotyping_arrays + label: derived_from + target_type: aliquot + multiplicity: many_to_one + required: false + +required: + - type + - submitter_id + - file_name + - file_size + - md5sum + - data_category + - data_type + - data_format + - experimental_strategy + - platform + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +properties: + $ref: "_definitions.yaml#/data_file_properties" + + data_category: + term: + $ref: "_terms.yaml#/data_category" + enum: + - Copy Number Variation + + data_type: + $ref: "_terms.yaml#/data_type" + enum: + - Raw Intensities + + data_format: + $ref: "_terms.yaml#/data_format" + enum: + - CEL + + experimental_strategy: + $ref: "_terms.yaml#/experimental_strategy" + enum: + - Genotyping Array + + platform: + $ref: "_terms.yaml#/platform" + enum: + - Affymetrix + - Affymetrix SNP 6.0 + + aliquots: + $ref: "_definitions.yaml#/to_one" + core_metadata_collections: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_methylation.yaml b/gdcdictionary/schemas/submitted_methylation.yaml index e4efc72..d87af4b 100644 --- a/gdcdictionary/schemas/submitted_methylation.yaml +++ b/gdcdictionary/schemas/submitted_methylation.yaml @@ -70,8 +70,6 @@ properties: term: $ref: "_terms.yaml#/data_format" enum: - - ARR - - CEL - IDAT assay_method: