[WIP] Adding concepts from the BMEG schema

schemas/graph/Exon.yaml

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+$schema: https://json-schema.org/draft/2020-12/schema
+$id: Exon
+title: Exon
+type: object
+description: An exon - Exon is a region of the transcript sequence within a gene which
+  is not removed from the primary RNA transcript by RNA splicing.
+links:
+  - rel: transcripts_Transcript
+    href: Transcript/{id}
+    templateRequired:
+      - id
+    targetSchema:
+      $ref: Transcript.yaml
+    templatePointers:
+      id: /transcripts/-/id
+    targetHints:
+      directionality:
+        - outbound
+      multiplicity:
+        - has_many
+      backref:
+        - transcripts_exon
+properties:
+  id:
+    type: string
+    element_property: true
+  genome:
+    element_property: true
+    type: string
+    description: Reference to a genome build
+    enum:
+      - GRCh37
+      - GRCh38
+  chromosome:
+    element_property: true
+    type: string
+    description: Reference to a chromosome
+    pattern: ^(chr).*$
+  start:
+    type: integer
+    element_property: true
+  end:
+    type: integer
+    element_property: true
+  strand:
+    element_property: true
+    type: string
+    description: Reference to a chromosome strand
+    enum:
+      - +
+      - '-'
+  type:
+    type: string
+    element_property: true
+  transcripts:
+    type: array
+    items:
+      $ref: Transcript.yaml
+    element_property: true
+    backref: transcripts_exon
+  exonId:
+    type: string
+    element_property: true
+  projectId:
+    element_property: true
+    type: string
+  submitterId:
+    type: string
+    element_property: true
+  createdDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  updatedDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  resourceType:
+    default: exon
+    type: string
+    description: One of the resource types defined as part of BMEG

schemas/graph/Gene.yaml

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+$schema: https://json-schema.org/draft/2020-12/schema
+$id: Gene
+title: Gene
+type: object
+description: A region (or regions) that includes all of the sequence elements necessary
+  to encode a functional transcript. A gene may include regulatory regions, transcribed
+  regions and/or other functional sequence regions. A gene may be considered as a
+  unit of inheritance.
+links: []
+properties:
+  id:
+    type: string
+    element_property: true
+  description:
+    type: string
+    element_property: true
+  symbol:
+    type: string
+    element_property: true
+  genome:
+    element_property: true
+    type: string
+    description: Reference to a genome build
+    enum:
+      - GRCh37
+      - GRCh38
+  chromosome:
+    element_property: true
+    type: string
+    description: Reference to a chromosome
+    pattern: ^(chr).*$
+  start:
+    type: integer
+    element_property: true
+  end:
+    type: integer
+    element_property: true
+  strand:
+    element_property: true
+    type: string
+    description: Reference to a chromosome strand
+    enum:
+      - +
+      - '-'
+  type:
+    type: string
+    element_property: true
+  projectId:
+    element_property: true
+    type: string
+  submitterId:
+    type: string
+    element_property: true
+  createdDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  updatedDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  resourceType:
+    default: gene
+    type: string
+    description: One of the resource types defined as part of BMEG

schemas/graph/GeneExpression.yaml

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+$id: GeneExpression
+$schema: https://json-schema.org/draft/2020-12/schema
+description: Gene level expression values for an aliquot - The process in which a
+  genes sequence is converted into a mature gene product (protein or RNA). This includes
+  the production of an RNA transcript and its processing, as well as translation and
+  maturation for protein-coding genes.
+links:
+- href: Specimen/{id}
+  rel: specimen_Specimen
+  targetHints:
+    backref:
+    - specimen_geneexpression
+    directionality:
+    - outbound
+    multiplicity:
+    - has_one
+  targetSchema:
+    $ref: Specimen.yaml
+  templatePointers:
+    id: /specimen/-/id
+  templateRequired:
+  - id
+properties:
+  createdDateTime:
+    element_property: true
+    format: date-time
+    type: string
+  id:
+    element_property: true
+    systemAlias: node_id
+    type: string
+  method:
+    element_property: true
+    type: string
+  metric:
+    description: Expression metric
+    element_property: true
+    enum:
+    - TPM
+    - TPM_GENE
+    - RPKM
+    - FPKM
+    - RAW_COUNT
+    - RMA
+    type: string
+  projectId:
+    element_property: true
+    type: string
+  resourceType:
+    default: gene_expression
+    description: One of the resource types defined as part of BMEG
+    type: string
+  specimen:
+    backref: specimen_geneexpression
+    element_property: true
+    items:
+      $ref: Specimen.yaml
+    type: array
+  submitterId:
+    element_property: true
+    type: string
+  type:
+    element_property: true
+    type: string
+  updatedDateTime:
+    element_property: true
+    format: date-time
+    type: string
+  values:
+    additionalProperties:
+      type: number
+    element_property: true
+    propertyNames:
+      pattern: ^ENSG[0-9]+
+    type: object
+title: GeneExpression
+type: object

schemas/graph/GeneOntologyTerm.yaml

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+$schema: https://json-schema.org/draft/2020-12/schema
+$id: GeneOntologyTerm
+title: GeneOntologyTerm
+type: object
+description: The Gene Ontology project provides an ontology of defined terms representing  gene
+  product properties.
+links:
+  - rel: genes_Gene
+    href: Gene/{id}
+    templateRequired:
+      - id
+    targetSchema:
+      $ref: Gene.yaml
+    templatePointers:
+      id: /genes/-/id
+    targetHints:
+      directionality:
+        - outbound
+      multiplicity:
+        - has_many
+      backref:
+        - genes_gene_ontology_term
+  - rel: childTerms_GeneOntologyTer
+    href: GeneOntologyTerm/{id}
+    templateRequired:
+      - id
+    targetSchema:
+      $ref: GeneOntologyTerm.yaml
+    templatePointers:
+      id: /childTerms/-/id
+    targetHints:
+      directionality:
+        - outbound
+      multiplicity:
+        - has_many
+      backref:
+        - childTerms_gene_ontology_term
+properties:
+  name:
+    type: string
+    element_property: true
+  namespace:
+    type: string
+    element_property: true
+  definition:
+    type: string
+    element_property: true
+  synonym:
+    type: array
+    element_property: true
+  xref:
+    type: array
+    items:
+      type: string
+    element_property: true
+  id:
+    type: string
+    systemAlias: node_id
+    element_property: true
+  type:
+    type: string
+    element_property: true
+  genes:
+    type: array
+    items:
+      $ref: Gene.yaml
+    element_property: true
+    backref: genes_gene_ontology_term
+  goId:
+    type: string
+    element_property: true
+  projectId:
+    element_property: true
+    type: string
+  submitterId:
+    type: string
+    element_property: true
+  createdDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  updatedDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  childTerms:
+    type: array
+    items:
+      $ref: GeneOntologyTerm.yaml
+    element_property: true
+    backref: childTerms_gene_ontology_term
+  resourceType:
+    default: gene_ontology_term
+    type: string
+    description: One of the resource types defined as part of BMEG

schemas/graph/Publication.yaml

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+$schema: https://json-schema.org/draft/2020-12/schema
+$id: Publication
+title: Publication
+type: object
+description: A publication - In academic publishing, a scientific journal is a periodical
+  publication intended to further the progress of science, usually by sharing findings
+  from research with readers.
+links: []
+properties:
+  id:
+    type: string
+    systemAlias: node_id
+    element_property: true
+  url:
+    type: string
+    element_property: true
+  abstract:
+    type: string
+    element_property: true
+  author:
+    type: array
+    element_property: true
+  citation:
+    type: array
+    element_property: true
+  date:
+    type: string
+    element_property: true
+  text:
+    type: string
+    element_property: true
+  title:
+    type: string
+    element_property: true
+  type:
+    type: string
+    element_property: true
+  projectId:
+    element_property: true
+    type: string
+  submitterId:
+    type: string
+    element_property: true
+  createdDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  updatedDateTime:
+    element_property: true
+    type: string
+    format: date-time
+  resourceType:
+    default: publication
+    type: string
+    description: One of the resource types defined as part of BMEG