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Class: EntityToPhenotypicFeatureAssociationMixin

classDiagram class EntityToPhenotypicFeatureAssociationMixin FrequencyQuantifier <|-- EntityToPhenotypicFeatureAssociationMixin EntityToFeatureOrDiseaseQualifiersMixin <|-- EntityToPhenotypicFeatureAssociationMixin EntityToPhenotypicFeatureAssociationMixin <|-- PhenotypicFeatureToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- ExposureEventToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- DiseaseToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- CaseToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- BehaviorToBehavioralFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GeneToDiseaseOrPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GeneToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- VariantToPhenotypicFeatureAssociation 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 : object_direction_qualifier EntityToPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : object_direction_qualifier EntityToPhenotypicFeatureAssociationMixin : object_specialization_qualifier EntityToPhenotypicFeatureAssociationMixin : predicate EntityToPhenotypicFeatureAssociationMixin : qualified_predicate EntityToPhenotypicFeatureAssociationMixin : sex_qualifier EntityToPhenotypicFeatureAssociationMixin --|> BiologicalSex : sex_qualifier EntityToPhenotypicFeatureAssociationMixin : subject EntityToPhenotypicFeatureAssociationMixin --|> NamedThing : subject EntityToPhenotypicFeatureAssociationMixin : subject_aspect_qualifier EntityToPhenotypicFeatureAssociationMixin : subject_direction_qualifier EntityToPhenotypicFeatureAssociationMixin --|> DirectionQualifierEnum : subject_direction_qualifier EntityToPhenotypicFeatureAssociationMixin : subject_specialization_qualifier

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
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		 direct
predicate:
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. 		1
PredicateType		 direct
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. 		1
PhenotypicFeature		 direct HP:0002487, WBPhenotype:0000180, MP:0001569
sex_qualifier:
a qualifier used in a phenotypic association to state whether the association is specific to a particular sex. 		0..1
BiologicalSex		 direct
disease_context_qualifier:
A context qualifier representing a disease or condition in which a relationship expressed in an association took place. 		0..1
Disease		 direct 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		 direct
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		 direct
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). 		0..1
String		 direct blood, cerebral cortext
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
String		 EntityToFeatureOrDiseaseQualifiersMixin 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		 EntityToFeatureOrDiseaseQualifiersMixin
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
String		 EntityToFeatureOrDiseaseQualifiersMixin 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		 EntityToFeatureOrDiseaseQualifiersMixin
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. 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
String		 EntityToFeatureOrDiseaseQualifiersMixin
frequency_qualifier:
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject 		0..1
FrequencyValue		 FrequencyQualifierMixin

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.
GeneToDiseaseOrPhenotypicFeatureAssociation None
GeneToPhenotypicFeatureAssociation None
VariantToPhenotypicFeatureAssociation None

LinkML Source

name: entity to phenotypic feature association mixin
from_schema: https://w3id.org/biolink/biolink-model
is_a: entity to feature or disease qualifiers mixin
mixin: true
mixins:
- frequency quantifier
slots:
- subject
- predicate
- object
- sex qualifier
- disease context qualifier
- subject specialization qualifier
- object specialization qualifier
- anatomical context 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