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.