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VariantToPopulationAssociation

An association between a variant and a population, where the variant has particular frequency in the population

classDiagram VariantToEntityAssociationMixin <|-- VariantToPopulationAssociation FrequencyQuantifier <|-- VariantToPopulationAssociation FrequencyQualifierMixin <|-- VariantToPopulationAssociation Association <|-- VariantToPopulationAssociation VariantToPopulationAssociation : aggregator_knowledge_source VariantToPopulationAssociation : category VariantToPopulationAssociation : description VariantToPopulationAssociation : frequency_qualifier VariantToPopulationAssociation : has_attribute VariantToPopulationAssociation : has_count VariantToPopulationAssociation : has_evidence VariantToPopulationAssociation : has_percentage VariantToPopulationAssociation : has_quotient VariantToPopulationAssociation : has_total VariantToPopulationAssociation : id VariantToPopulationAssociation : iri VariantToPopulationAssociation : knowledge_source VariantToPopulationAssociation : name VariantToPopulationAssociation : negated VariantToPopulationAssociation : object VariantToPopulationAssociation : original_knowledge_source VariantToPopulationAssociation : predicate VariantToPopulationAssociation : primary_knowledge_source VariantToPopulationAssociation : publications VariantToPopulationAssociation : qualifiers VariantToPopulationAssociation : source VariantToPopulationAssociation : subject VariantToPopulationAssociation : timepoint VariantToPopulationAssociation : type

Parent Classes

  • Entity
    • Association
      • VariantToPopulationAssociation [ variant to entity association mixin frequency quantifier frequency qualifier 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_count number in object population that carry a particular allele, aka allele count
has_evidence connects an association to an instance of supporting evidence
has_percentage equivalent to has quotient multiplied by 100
has_quotient frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency
has_total number all populations that carry a particular allele, aka allele number
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 the population that is observed to have the frequency
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
source None
subject an allele that has a certain frequency in a given population
timepoint a point in time
type None

Mappings

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