information-resource.yaml

---
id: https://w3id.org/biolink/biolink-model
name: Biolink-Model
description: Entity and association taxonomy and datamodel for life-sciences data
license: https://creativecommons.org/publicdomain/zero/1.0/

# Version should be kept in sync with primary Git repository release tag

version: 3.5.4


## ------------
##
## PREFIXES
## ------------
# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification
# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld
# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following
# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's
# which should ideally be repaired in one of the precedence lists.
#
# 1. The following 'prefixes:' delimited list has first precedence in resolution.
#
prefixes:
  biolink: 'https://w3id.org/biolink/vocab/'
  linkml: 'https://w3id.org/linkml/'
  infores: 'https://w3id.org/biolink/vocab/'

imports:
  - linkml:types

default_prefix: infores
default_range: string

default_curi_maps:
  - obo_context
  - idot_context
  - monarch_context
  - semweb_context

emit_prefixes:
  - rdf
  - rdfs
  - xsd
  - skos
  - oboInOwl
  - BIOGRID
  - SO

classes:
  InformationResourceContainer:
    tree_root: true
    description: >-
      A collection of information resources
    slots:
      - information_resources

  InformationResource:
    aliases: ['knowledgebase']
    slots:
      - status
      - name
      - id
      - xref
      - synonym
      - description
      - knowledge level
      - agent type
    description: >-
      A database or knowledgebase and its supporting ecosystem of interfaces 
      and services that deliver content to consumers (e.g. web portals, APIs, 
      query endpoints, streaming services, data downloads, etc.).
      A single Information Resource by this definition may span many different datasets or
      databases, and include many access endpoints and user
      interfaces. Information Resources include project-specific resources
      such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.

slots:

  status:
    description: the status of the infores identifier, the default is "released"
    range: InformationResourceStatusEnum

  information_resources:
    description: a collection of information resources
    multivalued: true
    range: InformationResource
    inlined_as_list: true

  name:
    aliases: [ 'label', 'display name', 'title' ]
    description: >-
      A human-readable name for an attribute or entity.
    slot_uri: rdfs:label
    exact_mappings:
      - gff3:Name
      - gpi:DB_Object_Name
    narrow_mappings:
      - dct:title
      - WIKIDATA_PROPERTY:P1476

  id:
    identifier: true
    description: >-
      A unique identifier for an entity.
      Must be either a CURIE shorthand for a URI or a complete URI
    required: true
    exact_mappings:
      - AGRKB:primaryId
      - gff3:ID
      - gpi:DB_Object_ID

  xref:
    aliases: [ 'dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls' ]
    description: >-
      A database cross reference or alternative identifier for a NamedThing or edge between two 
      NamedThings.  This property should point to a database record or webpage that supports the existence of the edge, or 
      gives more detail about the edge. This property can be used on a node or edge to provide multiple
      URIs or CURIE cross references.
    multivalued: true
    narrow_mappings:
      - gff3:Dbxref
      - gpi:DB_Xrefs

  synonym:
    aliases: [ 'alias' ]
    description: >-
      Alternate human-readable names for a thing
    multivalued: true
    narrow_mappings:
      - skos:altLabel
      - gff3:Alias
      - AGRKB:synonyms
      - gpi:DB_Object_Synonyms
      # TODO: RTX contributed terms mapped here... May need review?
      - HANCESTRO:0330
      - IAO:0000136
      - RXNORM:has_tradename

  description:
  knowledge level:
  agent type:

enums:
  InformationResourceStatusEnum:
    permissible_values:
      released:
      deprecated:
      draft:
      modified: