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
- Entity
- Association
- GeneToDiseaseOrPhenotypicFeatureAssociation [ EntityToPhenotypicFeatureAssociationMixin GeneToEntityAssociationMixin]
- Association
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