Update BDC data model to further support genomic data

gdcdictionary/schemas/reference_file.yaml

@@ -87,6 +87,7 @@ properties:
       - ALT
       - AMB
       - ANN
+      - ARR
       - AVRO
       - BCF
       - BED

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"

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"

gdcdictionary/schemas/submitted_methylation.yaml

@@ -70,8 +70,6 @@ properties:
     term:
       $ref: "_terms.yaml#/data_format"
     enum:
-      - ARR
-      - CEL
       - IDAT
 
   assay_method: