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Class: GenotypeToPhenotypicFeatureAssociation

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

URI: biolink:GenotypeToPhenotypicFeatureAssociation

classDiagram class GenotypeToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation GenotypeToEntityAssociationMixin <|-- GenotypeToPhenotypicFeatureAssociation Association <|-- GenotypeToPhenotypicFeatureAssociation GenotypeToPhenotypicFeatureAssociation : aggregator_knowledge_source GenotypeToPhenotypicFeatureAssociation : category GenotypeToPhenotypicFeatureAssociation : description GenotypeToPhenotypicFeatureAssociation : frequency_qualifier GenotypeToPhenotypicFeatureAssociation : has_attribute GenotypeToPhenotypicFeatureAssociation --|> attribute : has_attribute GenotypeToPhenotypicFeatureAssociation : has_count GenotypeToPhenotypicFeatureAssociation : has_evidence GenotypeToPhenotypicFeatureAssociation --|> evidence type : has_evidence GenotypeToPhenotypicFeatureAssociation : has_percentage GenotypeToPhenotypicFeatureAssociation : has_quotient GenotypeToPhenotypicFeatureAssociation : has_total GenotypeToPhenotypicFeatureAssociation : id GenotypeToPhenotypicFeatureAssociation : iri GenotypeToPhenotypicFeatureAssociation : knowledge_source GenotypeToPhenotypicFeatureAssociation : name GenotypeToPhenotypicFeatureAssociation : negated GenotypeToPhenotypicFeatureAssociation : object GenotypeToPhenotypicFeatureAssociation --|> phenotypic feature : object GenotypeToPhenotypicFeatureAssociation : object_category GenotypeToPhenotypicFeatureAssociation --|> ontology class : object_category GenotypeToPhenotypicFeatureAssociation : object_category_closure GenotypeToPhenotypicFeatureAssociation --|> ontology class : object_category_closure GenotypeToPhenotypicFeatureAssociation : object_closure GenotypeToPhenotypicFeatureAssociation : object_label_closure GenotypeToPhenotypicFeatureAssociation : object_namespace GenotypeToPhenotypicFeatureAssociation : onset_qualifier GenotypeToPhenotypicFeatureAssociation --|> onset : onset_qualifier GenotypeToPhenotypicFeatureAssociation : original_object GenotypeToPhenotypicFeatureAssociation : original_predicate GenotypeToPhenotypicFeatureAssociation : original_subject GenotypeToPhenotypicFeatureAssociation : predicate GenotypeToPhenotypicFeatureAssociation : primary_knowledge_source GenotypeToPhenotypicFeatureAssociation : publications GenotypeToPhenotypicFeatureAssociation --|> publication : publications GenotypeToPhenotypicFeatureAssociation : qualifiers GenotypeToPhenotypicFeatureAssociation --|> ontology class : qualifiers GenotypeToPhenotypicFeatureAssociation : retrieval_source_ids GenotypeToPhenotypicFeatureAssociation --|> retrieval source : retrieval_source_ids GenotypeToPhenotypicFeatureAssociation : severity_qualifier GenotypeToPhenotypicFeatureAssociation --|> severity value : severity_qualifier GenotypeToPhenotypicFeatureAssociation : sex_qualifier GenotypeToPhenotypicFeatureAssociation --|> biological sex : sex_qualifier GenotypeToPhenotypicFeatureAssociation : subject GenotypeToPhenotypicFeatureAssociation --|> genotype : subject GenotypeToPhenotypicFeatureAssociation : subject_category GenotypeToPhenotypicFeatureAssociation --|> ontology class : subject_category GenotypeToPhenotypicFeatureAssociation : subject_category_closure GenotypeToPhenotypicFeatureAssociation --|> ontology class : subject_category_closure GenotypeToPhenotypicFeatureAssociation : subject_closure GenotypeToPhenotypicFeatureAssociation : subject_label_closure GenotypeToPhenotypicFeatureAssociation : subject_namespace GenotypeToPhenotypicFeatureAssociation : timepoint GenotypeToPhenotypicFeatureAssociation : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sex_qualifier 0..1
BiologicalSex
a qualifier used in a phenotypic association to state whether the association... EntityToPhenotypicFeatureAssociationMixin
subject 1..1
Genotype
genotype that is associated with the phenotypic feature Association
predicate 1..1
PredicateType
A high-level grouping for the relationship type Association
object 1..1
PhenotypicFeature
connects an association to the object of the association Association
negated 0..1
Boolean
if set to true, then the association is negated i Association
qualifiers 0..*
OntologyClass
connects an association to qualifiers that modify or qualify the meaning of t... Association
publications 0..*
Publication
One or more publications that report the statement expressed in an Associati... Association
has_evidence 0..*
EvidenceType
connects an association to an instance of supporting evidence Association
knowledge_source 0..1
String
An Information Resource from which the knowledge expressed in an Association ... Association
primary_knowledge_source 0..1
String
The most upstream source of the knowledge expressed in an Association that an... Association
aggregator_knowledge_source 0..*
String
An intermediate aggregator resource from which knowledge expressed in an Asso... Association
timepoint 0..1
TimeType
a point in time Association
original_subject 0..1
String
used to hold the original subject of a relation (or predicate) that an extern... Association
original_predicate 0..1
Uriorcurie
used to hold the original relation/predicate that an external knowledge sourc... Association
original_object 0..1
String
used to hold the original object of a relation (or predicate) that an externa... Association
subject_category 0..1
OntologyClass
Used to hold the biolink class/category of an association Association
object_category 0..1
OntologyClass
Used to hold the biolink class/category of an association Association
subject_closure 0..*
String
Used to hold the subject closure of an association Association
object_closure 0..*
String
Used to hold the object closure of an association Association
subject_category_closure 0..*
OntologyClass
Used to hold the subject category closure of an association Association
object_category_closure 0..*
OntologyClass
Used to hold the object category closure of an association Association
subject_namespace 0..1
String
Used to hold the subject namespace of an association Association
object_namespace 0..1
String
Used to hold the object namespace of an association Association
subject_label_closure 0..*
String
Used to hold the subject label closure of an association Association
object_label_closure 0..*
String
Used to hold the object label closure of an association Association
retrieval_source_ids 0..*
RetrievalSource
A list of retrieval sources that served as a source of knowledge expressed in... Association
id 1..1
String
A unique identifier for an entity Entity
iri 0..1
IriType
An IRI for an entity Entity
category 0..*
CategoryType
Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String
rdf:type of biolink:Association should be fixed at rdf:Statement Entity
name 0..1
LabelType
A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText
a human-readable description of an entity Entity
has_attribute 0..*
Attribute
connects any entity to an attribute Entity
has_count 0..1
Integer
number of things with a particular property FrequencyQuantifier
has_total 0..1
Integer
total number of things in a particular reference set FrequencyQuantifier
has_quotient 0..1
Double
FrequencyQuantifier
has_percentage 0..1
Double
equivalent to has quotient multiplied by 100 FrequencyQuantifier
severity_qualifier 0..1
SeverityValue
a qualifier used in a phenotypic association to state how severe the phenotyp... EntityToFeatureOrDiseaseQualifiersMixin
onset_qualifier 0..1
Onset
a qualifier used in a phenotypic association to state when the phenotype appe... EntityToFeatureOrDiseaseQualifiersMixin
frequency_qualifier 0..1
FrequencyValue
a qualifier used in a phenotypic association to state how frequent the phenot... FrequencyQualifierMixin

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:GenotypeToPhenotypicFeatureAssociation
native biolink:GenotypeToPhenotypicFeatureAssociation

LinkML Source

Direct

name: genotype to phenotypic feature association
description: Any association between one genotype and a phenotypic feature, where
  having the genotype confers the phenotype, either in isolation or through environment
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
mixins:
- entity to phenotypic feature association mixin
- genotype to entity association mixin
slot_usage:
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: has phenotype
  subject:
    name: subject
    description: genotype that is associated with the phenotypic feature
    domain_of:
    - association
    range: genotype
defining_slots:
- subject
- object