URIs and Mappings

exact_mappings

The exact_mappings slot can be used to define external concepts, predicates, or properties which are considered to be exact mappings to the class (or slot) being defined.

  same as:
    is_a: exact match
    description: >-
      holds between two entities that are considered equivalent to each other
    in_subset:
      - translator_minimal
    exact_mappings:
      - owl:sameAs
      - skos:exactMatch
      - WIKIDATA_PROPERTY:P2888
      - CHEMBL.MECHANISM:equivalent_to
      - MONDO:equivalentTo

Here we define a list of 5 predicates that are semantically equivalent to the Biolink Model predicate slot same as.

close_mappings

The close_mappings slot can be used to define external concepts, predicates, or properties which are considered to be close mappings to the class (or slot) being defined.

  same as:
    is_a: exact match
    description: >-
      holds between two entities that are considered equivalent to each other
    in_subset:
      - translator_minimal
    exact_mappings:
      - owl:sameAs
      - skos:exactMatch
      - WIKIDATA_PROPERTY:P2888
      - CHEMBL.MECHANISM:equivalent_to
      - MONDO:equivalentTo
    close_mappings:
      - owl:equivalentClass

Here we define owl:equivalentClass as being a close match to the Biolink Model predicate slot same as.

narrow_mappings

The narrow_mappings slot can be used to define external concepts, predicates, or properties which are considered to be narrow mappings to the class (or slot) being defined.

  same as:
    is_a: exact match
    description: >-
      holds between two entities that are considered equivalent to each other
    in_subset:
      - translator_minimal
    close_mappings:
      - owl:equivalentClass
    exact_mappings:
      - owl:sameAs
      - skos:exactMatch
      - WIKIDATA_PROPERTY:P2888
      - CHEMBL.MECHANISM:equivalent_to
      - MONDO:equivalentTo
    narrow_mappings:
      - DRUGBANK:external-identifier

Here we define DRUGBANK:external-identifier as being a narrow match to the predicate slot same as.

By narrow we mean that the scope of DRUGBANK:external-identifier is more narrower and restrictive than same as.

If we were to create a new predicate slot as a proxy for DRUGBANK:external-identifier then that new slot would be a child of same as.

broad_mappings

The broad_mappings slot can be used to define external concepts, predicates, or properties which are considered to be broad mappings to the class (or slot) being defined.

  in complex with:
    description: >-
      holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
    is_a: coexists with
    domain: gene or gene product
    range: gene or gene product
    in_subset:
      - translator_minimal
    broad_mappings:
      - SIO:010285

Here we define SIO:010285 (molecular complex formation) as a broad mapping to the predicate slot in complex with.

By broad we mean that the scope of SIO:010285 is more broad and relaxed than in complex with.

If we were to create a new predicate slot as a proxy for SIO:010285 then that new slot would be a parent of in complex with.

slot_uri

The slot_uri slot can be used to define a canonical URI that is the true representation for that particular slot. That is, the value of slot_uri can be used interchangably with the slot being defined.

  name:
    is_a: node property
    aliases: ['label', 'display name']
    domain: named thing
    range: label type
    slot_uri: rdfs:label

Here we define rdfs:label as the canonical URI for the property slot name. When serializing a graph into RDF, the name of an instance of entity class named thing will be represented using rdfs:label instead of biolink:name.

This is to ensure that we use certain core RDF predicates as is.

id_prefixes

The id_prefixes slot can be used to define a list of valid ID prefixes that instances of this class ought to have as part of their CURIE.

The order of the list matters since its a prioritized list with the ID prefix with the highest priority appearing at the top of the list.

  gene:
    is_a: gene or gene product
    aliases: ['locus']
    slots:
      - id
      - name
      - symbol
      - description
      - synonym
      - xref
    mappings:
      - SO:0000704
      - SIO:010035
      - WIKIDATA:Q7187
    id_prefixes:
      - NCBIGene
      - ENSEMBL
      - HGNC
      - UniProtKB
      - MGI
      - ZFIN
      - dictyBase
      - WB
      - WormBase
      - FlyBase
      - FB
      - RGD
      - SGD
      - PomBase

Here we define the entity class gene to have a list of ID prefixes with NCBIGene having the highest priority.