genome_annotation.yaml

id: https://identifiers.org/brain-bican/genome-annotation-schema
name: genome-annotation-schema
title: Genome Annotation Schema
description: |-
  The Genome Annotation schema is designed to represent types and relationships of an organism's annotated genome.
  
prefixes:
  linkml: https://w3id.org/linkml/
  bican: https://identifiers.org/brain-bican/vocab/
  spdx: http://spdx.org/rdf/terms#
  schema: http://schema.org/
  ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
  NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/
  prov: http://www.w3.org/ns/prov#

imports:
  - linkml:types
  - bican_biolink
default_range: string
default_prefix: bican

classes:
  gene annotation:
    is_a: gene
    description: >-
      An annotation describing the location, boundaries, and functions of 
      individual genes within a genome annotation.
    slots:
      - molecular type
      - source id
    attributes:
      referenced in: 
        description: The genome annotation that this gene annotation was referenced from.
        required: true
        inlined: true
        any_of:
          - range: genome annotation
          - range: string
    id_prefixes:
      - ENSEMBL
      - MGI
      - NCBIGene

  genome annotation:
    is_a: genome
    description: >-
      Location and nomenclature of genes and all of the coding regions in a genome assembly 
      and the classification of genes and transcripts into types.
    slots:
      - version
      - digest
      - content_url
      - authority
    attributes:
      reference assembly:
        description: The reference genome assembly that this genome annotation was created from.
        required: true
        inlined: true
        any_of:
          - range: genome assembly
          - range: string

  genome assembly:
    is_a: named thing
    mixins:
      - thing with taxon
    description: >-
      Genome assembly to contain version and label information
    slots:
      - version
      - strain

  checksum:
    is_a: entity
    description: >-
      Checksum values associated with digital entities.
    slots:
      - checksum algorithm
    attributes:
      value: 
        description: The checksum value obtained from a specific cryotographic hash function.

  annotation collection:
    tree_root: true
    attributes:
      annotations:
        multivalued: true
        inlined_as_list: true
        range: gene annotation
      genome_annotations:
        multivalued: true
        inlined_as_list: true
        range: genome annotation
      genome_assemblies:
        multivalued: true
        inlined_as_list: true
        range: genome assembly


slots:
  molecular type:
    any_of:
      - range: BioType
      - range: string

  digest:
    description: Stores checksum information. 
    multivalued: true
    inlined_as_list: true
    any_of:
      - range: checksum
      - range: string

  content_url:
    slot_uri: schema:url
    multivalued: true

  authority:
    description: The organization responsible for publishing the data. 
    range: AuthorityType

  checksum algorithm:
    description: The type of cryptographic hash function used to calculate the checksum value.
    range: DigestType

  source id:
    description: The authority specific identifier. 
    slot_uri: schema:identifier
  
  strain:
    description: The genetic variant or subtype of a species or organism. 


enums:
  DigestType:
    permissible_values:
      spdx:checksumAlgorithm_sha1:
        title: SHA1
        meaning: spdx:checksumAlgorithm_sha1
      spdx:checksumAlgorithm_md5:
        title: MD5
        meaning: spdx:checksumAlgorithm_md5
      spdx:checksumAlgorithm_sha256:
        title: SHA256
        meaning: spdx:checksumAlgorithm_sha256

  BioType:
    permissible_values:
      protein_coding:
      noncoding:

  AuthorityType: 
    permissible_values:
      ENSEMBL:
      NCBI: