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Class: PhenotypicFeatureToEntityAssociationMixin

classDiagram class PhenotypicFeatureToEntityAssociationMixin FrequencyQuantifier <|-- PhenotypicFeatureToEntityAssociationMixin FeatureOrDiseaseQualifiersToEntityMixin <|-- PhenotypicFeatureToEntityAssociationMixin PhenotypicFeatureToEntityAssociationMixin <|-- PhenotypicFeatureToPhenotypicFeatureAssociation PhenotypicFeatureToEntityAssociationMixin <|-- PhenotypicFeatureToDiseaseAssociation PhenotypicFeatureToEntityAssociationMixin : frequency_qualifier PhenotypicFeatureToEntityAssociationMixin : has_count PhenotypicFeatureToEntityAssociationMixin : has_percentage PhenotypicFeatureToEntityAssociationMixin : has_quotient PhenotypicFeatureToEntityAssociationMixin : has_total PhenotypicFeatureToEntityAssociationMixin : object PhenotypicFeatureToEntityAssociationMixin --|> NamedThing : object PhenotypicFeatureToEntityAssociationMixin : object_aspect_qualifier PhenotypicFeatureToEntityAssociationMixin : object_direction_qualifier PhenotypicFeatureToEntityAssociationMixin --|> DirectionQualifierEnum : object_direction_qualifier PhenotypicFeatureToEntityAssociationMixin : predicate PhenotypicFeatureToEntityAssociationMixin : qualified_predicate PhenotypicFeatureToEntityAssociationMixin : sex_qualifier PhenotypicFeatureToEntityAssociationMixin --|> BiologicalSex : sex_qualifier PhenotypicFeatureToEntityAssociationMixin : subject PhenotypicFeatureToEntityAssociationMixin --|> PhenotypicFeature : subject PhenotypicFeatureToEntityAssociationMixin : subject_aspect_qualifier PhenotypicFeatureToEntityAssociationMixin : subject_direction_qualifier PhenotypicFeatureToEntityAssociationMixin --|> DirectionQualifierEnum : subject_direction_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
String		 FeatureOrDiseaseQualifiersToEntityMixin 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		 FeatureOrDiseaseQualifiersToEntityMixin
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		 FeatureOrDiseaseQualifiersToEntityMixin 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		 FeatureOrDiseaseQualifiersToEntityMixin
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		 FeatureOrDiseaseQualifiersToEntityMixin
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
PhenotypicFeature		 FrequencyQualifierMixin HP:0002487, WBPhenotype:0000180, MP:0001569
predicate:
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. 		1
PredicateType		 FrequencyQualifierMixin
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
NamedThing		 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.
PhenotypicFeatureToDiseaseAssociation None

LinkML Source

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