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Class: EntityToPhenotypicFeatureAssociationMixin

Description: A mixin applied to any association whose object (target node) is a phenotypic feature.
classDiagram class EntityToPhenotypicFeatureAssociationMixin FrequencyQuantifier <|-- EntityToPhenotypicFeatureAssociationMixin EntityToDiseaseOrPhenotypicFeatureAssociationMixin <|-- EntityToPhenotypicFeatureAssociationMixin EntityToPhenotypicFeatureAssociationMixin <|-- PhenotypicFeatureToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- ExposureEventToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- DiseaseToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- CaseToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- BehaviorToBehavioralFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GeneToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- VariantToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- EntityToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin : anatomical_context_qualifier EntityToPhenotypicFeatureAssociationMixin : disease_context_qualifier EntityToPhenotypicFeatureAssociationMixin --|> Disease : disease_context_qualifier EntityToPhenotypicFeatureAssociationMixin : frequency_qualifier EntityToPhenotypicFeatureAssociationMixin : has_count EntityToPhenotypicFeatureAssociationMixin : has_percentage EntityToPhenotypicFeatureAssociationMixin : has_quotient EntityToPhenotypicFeatureAssociationMixin : has_total EntityToPhenotypicFeatureAssociationMixin : object EntityToPhenotypicFeatureAssociationMixin --|> PhenotypicFeature : object EntityToPhenotypicFeatureAssociationMixin : object_aspect_qualifier EntityToPhenotypicFeatureAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier EntityToPhenotypicFeatureAssociationMixin : object_direction_qualifier EntityToPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : object_direction_qualifier EntityToPhenotypicFeatureAssociationMixin : object_specialization_qualifier EntityToPhenotypicFeatureAssociationMixin : population_context_qualifier EntityToPhenotypicFeatureAssociationMixin --|> PopulationOfIndividualOrganisms : population_context_qualifier EntityToPhenotypicFeatureAssociationMixin : predicate EntityToPhenotypicFeatureAssociationMixin : qualified_predicate EntityToPhenotypicFeatureAssociationMixin : sex_qualifier EntityToPhenotypicFeatureAssociationMixin --|> BiologicalSex : sex_qualifier EntityToPhenotypicFeatureAssociationMixin : subject EntityToPhenotypicFeatureAssociationMixin --|> NamedThing : subject EntityToPhenotypicFeatureAssociationMixin : subject_aspect_qualifier EntityToPhenotypicFeatureAssociationMixin --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier EntityToPhenotypicFeatureAssociationMixin : subject_direction_qualifier EntityToPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : subject_direction_qualifier EntityToPhenotypicFeatureAssociationMixin : subject_specialization_qualifier

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
sex_qualifier:
a qualifier used in a phenotypic association to state whether the association is specific to a particular sex. 		0..1
BiologicalSex		 direct
has_count:
number of things with a particular property 		0..1
Integer		 FrequencyQuantifier
has_total:
total number of things in a particular reference set 		0..1
Integer		 FrequencyQuantifier
has_quotient:
None 		0..1
Double		 FrequencyQuantifier
has_percentage:
equivalent to has quotient multiplied by 100 		0..1
Double		 FrequencyQuantifier
subject_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin stability, abundance, expression, exposure
subject_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). 		0..1
DirectionQualifierEnum		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin increased, downregulated
object_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin stability, abundance, expression, exposure
object_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). 		0..1
DirectionQualifierEnum		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin increased, downregulated
qualified_predicate:
Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. 		0..1
Uriorcurie		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin biolink:causes
disease_context_qualifier:
A context qualifier representing a disease or condition in which a relationship expressed in an association took place. 		0..1
Disease		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin MONDO:0004979, MONDO:0005148
subject_specialization_qualifier:
A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. 		0..1
Uriorcurie		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin
object_specialization_qualifier:
A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. 		0..1
Uriorcurie		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin
anatomical_context_qualifier:
A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location). 		*
String		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin UBERON:0000178, UBERON:0000956, GO:0005794
population_context_qualifier:
a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. 		0..1
PopulationOfIndividualOrganisms		 EntityToDiseaseOrPhenotypicFeatureAssociationMixin
frequency_qualifier:
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject 		0..1
FrequencyValue		 FrequencyQualifierMixin
subject:
connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. 		1
NamedThing		 FrequencyQualifierMixin
predicate:
Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats 		1
Uriorcurie		 FrequencyQualifierMixin
object:
disease or phenotype 		1
PhenotypicFeature		 FrequencyQualifierMixin HP:0002487, WBPhenotype:0000180, MP:0001569

Mixin Usage

mixed into description
PhenotypicFeatureToPhenotypicFeatureAssociation Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
GenotypeToPhenotypicFeatureAssociation Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
ExposureEventToPhenotypicFeatureAssociation Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.
DiseaseToPhenotypicFeatureAssociation An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.
CaseToPhenotypicFeatureAssociation An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.
BehaviorToBehavioralFeatureAssociation An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.
GeneToPhenotypicFeatureAssociation An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature.
VariantToPhenotypicFeatureAssociation An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype.
EntityToPhenotypicFeatureAssociation An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, regulatory approvals, and number of cases.

LinkML Source

name: entity to phenotypic feature association mixin
description: A mixin applied to any association whose object (target node) is a phenotypic
  feature.
from_schema: https://w3id.org/biolink/vocab/
is_a: entity to disease or phenotypic feature association mixin
mixin: true
mixins:
- frequency quantifier
slots:
- sex qualifier
slot_usage:
  object:
    name: object
    examples:
    - value: HP:0002487
      description: Hyperkinesis
    - value: WBPhenotype:0000180
      description: axon morphology variant
    - value: MP:0001569
      description: abnormal circulating bilirubin level
    values_from:
    - upheno
    - hp
    - mp
    - wbphenotype
    range: phenotypic feature
defining_slots:
- subject
- predicate
- object