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GenotypeToPhenotypicFeatureAssociation

Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment

classDiagram EntityToPhenotypicFeatureAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation GenotypeToEntityAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation Association <|-- GenotypeToPhenotypicFeatureAssociation GenotypeToPhenotypicFeatureAssociation : aggregator_knowledge_source GenotypeToPhenotypicFeatureAssociation : category GenotypeToPhenotypicFeatureAssociation : description GenotypeToPhenotypicFeatureAssociation : frequency_qualifier GenotypeToPhenotypicFeatureAssociation : has_attribute GenotypeToPhenotypicFeatureAssociation : has_evidence GenotypeToPhenotypicFeatureAssociation : id GenotypeToPhenotypicFeatureAssociation : iri GenotypeToPhenotypicFeatureAssociation : knowledge_source GenotypeToPhenotypicFeatureAssociation : name GenotypeToPhenotypicFeatureAssociation : negated GenotypeToPhenotypicFeatureAssociation : object GenotypeToPhenotypicFeatureAssociation : onset_qualifier GenotypeToPhenotypicFeatureAssociation : original_knowledge_source GenotypeToPhenotypicFeatureAssociation : predicate GenotypeToPhenotypicFeatureAssociation : primary_knowledge_source GenotypeToPhenotypicFeatureAssociation : publications GenotypeToPhenotypicFeatureAssociation : qualifiers GenotypeToPhenotypicFeatureAssociation : severity_qualifier GenotypeToPhenotypicFeatureAssociation : sex_qualifier GenotypeToPhenotypicFeatureAssociation : source GenotypeToPhenotypicFeatureAssociation : subject GenotypeToPhenotypicFeatureAssociation : timepoint GenotypeToPhenotypicFeatureAssociation : type

Parent Classes

  • Entity
    • Association
      • GenotypeToPhenotypicFeatureAssociation [ entity to phenotypic feature association mixin genotype to entity association mixin]

Slots

Name Description
aggregator_knowledge_source An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.
category Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity, etc. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}
description a human-readable description of an entity
frequency_qualifier a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
has_attribute connects any entity to an attribute
has_evidence connects an association to an instance of supporting evidence
id A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
iri An IRI for an entity. This is determined by the id using expansion rules.
knowledge_source An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.
name A human-readable name for an attribute or entity.
negated if set to true, then the association is negated i.e. is not true
object connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
onset_qualifier a qualifier used in a phenotypic association to state when the phenotype appears is in the subject
original_knowledge_source None
predicate A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.
primary_knowledge_source The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).
publications connects an association to publications supporting the association
qualifiers connects an association to qualifiers that modify or qualify the meaning of that association
severity_qualifier a qualifier used in a phenotypic association to state how severe the phenotype is in the subject
sex_qualifier a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.
source None
subject genotype that is associated with the phenotypic feature
timepoint a point in time
type None

Mappings

Mapping Type Mapped Value
self ['biolink:GenotypeToPhenotypicFeatureAssociation']
native ['biolink:GenotypeToPhenotypicFeatureAssociation']