Skip to content

Class: GeneToDiseaseOrPhenotypicFeatureAssociation

URI: biolink:GeneToDiseaseOrPhenotypicFeatureAssociation

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject_aspect_qualifier 0..1
GeneOrGeneProductOrChemicalEntityAspectEnum
direct
object_direction_qualifier 0..1
DirectionQualifierEnum
direct
sex_qualifier 0..1
BiologicalSex
a qualifier used in a phenotypic association to state whether the association... EntityToPhenotypicFeatureAssociationMixin
subject 1..1
GeneOrGeneProduct
gene in which variation is correlated with the phenotypic feature Association
predicate 1..1
PredicateType
A high-level grouping for the relationship type Association
object 1..1
DiseaseOrPhenotypicFeature
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

Comments

  • NCIT:R176 refers to the inverse relationship
  • for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype
  • if the relationship of the statement using this predicate is statistical in nature, please use associated with likelihood or one of its children.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self biolink:GeneToDiseaseOrPhenotypicFeatureAssociation
native biolink:GeneToDiseaseOrPhenotypicFeatureAssociation
narrow WBVocab:Gene-Phenotype-Association, dcid:DiseaseGeneAssociation, SIO:000983

LinkML Source

Direct

name: gene to disease or phenotypic feature association
comments:
- NCIT:R176 refers to the inverse relationship
- for use in describing the affect that the loss of function of a gene can have on
  exacerbating or ameliorating a symptom/phenotype
- if the relationship of the statement using this predicate is statistical in nature,
  please use `associated with likelihood` or one of its children.
from_schema: https://w3id.org/biolink/biolink-model
narrow_mappings:
- WBVocab:Gene-Phenotype-Association
- dcid:DiseaseGeneAssociation
- SIO:000983
is_a: association
mixins:
- entity to phenotypic feature association mixin
- gene to entity association mixin
slots:
- subject aspect qualifier
- object direction qualifier
slot_usage:
  subject:
    name: subject
    description: gene in which variation is correlated with the phenotypic feature
    examples:
    - value: HGNC:2197
      description: COL1A1 (Human)
    domain_of:
    - association
    range: gene or gene product
  subject aspect qualifier:
    name: subject aspect qualifier
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    - gene to disease or phenotypic feature association
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  object:
    name: object
    domain_of:
    - association
    range: disease or phenotypic feature
  object direction qualifier:
    name: object direction qualifier
    domain_of:
    - predicate mapping
    - gene to disease or phenotypic feature association
    - chemical entity or gene or gene product regulates gene association
    range: DirectionQualifierEnum
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: affects