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Class: GeneToDiseaseOrPhenotypicFeatureAssociation

classDiagram class GeneToDiseaseOrPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GeneToDiseaseOrPhenotypicFeatureAssociation GeneToEntityAssociationMixin <|-- GeneToDiseaseOrPhenotypicFeatureAssociation Association <|-- GeneToDiseaseOrPhenotypicFeatureAssociation GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToPhenotypicFeatureAssociation GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToDiseaseAssociation GeneToDiseaseOrPhenotypicFeatureAssociation : adjusted_p_value GeneToDiseaseOrPhenotypicFeatureAssociation : agent_type GeneToDiseaseOrPhenotypicFeatureAssociation --|> AgentTypeEnum : agent_type GeneToDiseaseOrPhenotypicFeatureAssociation : aggregator_knowledge_source GeneToDiseaseOrPhenotypicFeatureAssociation : anatomical_context_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : category GeneToDiseaseOrPhenotypicFeatureAssociation : deprecated GeneToDiseaseOrPhenotypicFeatureAssociation : description GeneToDiseaseOrPhenotypicFeatureAssociation : disease_context_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation --|> Disease : disease_context_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : frequency_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : has_attribute GeneToDiseaseOrPhenotypicFeatureAssociation --|> Attribute : has_attribute GeneToDiseaseOrPhenotypicFeatureAssociation : has_count GeneToDiseaseOrPhenotypicFeatureAssociation : has_evidence GeneToDiseaseOrPhenotypicFeatureAssociation --|> EvidenceType : has_evidence GeneToDiseaseOrPhenotypicFeatureAssociation : has_percentage GeneToDiseaseOrPhenotypicFeatureAssociation : has_quotient GeneToDiseaseOrPhenotypicFeatureAssociation : has_supporting_studies GeneToDiseaseOrPhenotypicFeatureAssociation --|> Study : has_supporting_studies GeneToDiseaseOrPhenotypicFeatureAssociation : has_total GeneToDiseaseOrPhenotypicFeatureAssociation : id GeneToDiseaseOrPhenotypicFeatureAssociation : iri GeneToDiseaseOrPhenotypicFeatureAssociation : knowledge_level GeneToDiseaseOrPhenotypicFeatureAssociation --|> KnowledgeLevelEnum : knowledge_level GeneToDiseaseOrPhenotypicFeatureAssociation : knowledge_source GeneToDiseaseOrPhenotypicFeatureAssociation : name GeneToDiseaseOrPhenotypicFeatureAssociation : negated GeneToDiseaseOrPhenotypicFeatureAssociation : object GeneToDiseaseOrPhenotypicFeatureAssociation --|> DiseaseOrPhenotypicFeature : object GeneToDiseaseOrPhenotypicFeatureAssociation : object_aspect_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : object_category GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : object_category GeneToDiseaseOrPhenotypicFeatureAssociation : object_category_closure GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : object_category_closure GeneToDiseaseOrPhenotypicFeatureAssociation : object_closure GeneToDiseaseOrPhenotypicFeatureAssociation : object_direction_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation --|> DirectionQualifierEnum : object_direction_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : object_label_closure GeneToDiseaseOrPhenotypicFeatureAssociation : object_namespace GeneToDiseaseOrPhenotypicFeatureAssociation : object_specialization_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : original_object GeneToDiseaseOrPhenotypicFeatureAssociation : original_predicate GeneToDiseaseOrPhenotypicFeatureAssociation : original_subject GeneToDiseaseOrPhenotypicFeatureAssociation : p_value GeneToDiseaseOrPhenotypicFeatureAssociation : predicate GeneToDiseaseOrPhenotypicFeatureAssociation : primary_knowledge_source GeneToDiseaseOrPhenotypicFeatureAssociation : publications GeneToDiseaseOrPhenotypicFeatureAssociation --|> Publication : publications GeneToDiseaseOrPhenotypicFeatureAssociation : qualified_predicate GeneToDiseaseOrPhenotypicFeatureAssociation : qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : qualifiers GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : qualifiers GeneToDiseaseOrPhenotypicFeatureAssociation : retrieval_source_ids GeneToDiseaseOrPhenotypicFeatureAssociation --|> RetrievalSource : retrieval_source_ids GeneToDiseaseOrPhenotypicFeatureAssociation : sex_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation --|> BiologicalSex : sex_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : subject GeneToDiseaseOrPhenotypicFeatureAssociation --|> GeneOrGeneProduct : subject GeneToDiseaseOrPhenotypicFeatureAssociation : subject_aspect_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : subject_category GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : subject_category GeneToDiseaseOrPhenotypicFeatureAssociation : subject_category_closure GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : subject_category_closure GeneToDiseaseOrPhenotypicFeatureAssociation : subject_closure GeneToDiseaseOrPhenotypicFeatureAssociation : subject_direction_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation --|> DirectionQualifierEnum : subject_direction_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : subject_label_closure GeneToDiseaseOrPhenotypicFeatureAssociation : subject_namespace GeneToDiseaseOrPhenotypicFeatureAssociation : subject_specialization_qualifier GeneToDiseaseOrPhenotypicFeatureAssociation : timepoint GeneToDiseaseOrPhenotypicFeatureAssociation : type

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
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
GeneOrGeneProductOrChemicalEntityAspectEnum		 direct 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		 direct
subject:
gene in which variation is correlated with the phenotypic feature 		1
GeneOrGeneProduct		 GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association HGNC:2197
predicate:
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. 		1
PredicateType		 GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association
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
DiseaseOrPhenotypicFeature		 GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association 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		 EntityToPhenotypicFeatureAssociationMixin
disease_context_qualifier:
A context qualifier representing a disease or condition in which a relationship expressed in an association took place. 		0..1
Disease		 EntityToPhenotypicFeatureAssociationMixin, EntityToFeatureOrDiseaseQualifiersMixin 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		 EntityToPhenotypicFeatureAssociationMixin
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		 EntityToPhenotypicFeatureAssociationMixin
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		 EntityToPhenotypicFeatureAssociationMixin blood, cerebral cortext
negated:
if set to true, then the association is negated i.e. is not true 		0..1
Boolean		 Association
qualifier:
grouping slot for all qualifiers on an edge. useful for testing compliance with association classes 		0..1
String		 Association
qualifiers:
connects an association to qualifiers that modify or qualify the meaning of that association 		*
OntologyClass		 Association
publications:
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. 		*
Publication		 Association
has_evidence:
connects an association to an instance of supporting evidence 		*
EvidenceType		 Association
knowledge_source:
An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property. 		0..1
String		 Association
primary_knowledge_source:
The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to capture non-primary sources. 		0..1
String		 Association
aggregator_knowledge_source:
An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form. 		*
String		 Association
knowledge_level:
Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true. 		1
KnowledgeLevelEnum		 Association knowledge_assertion, prediction, statistical_association
agent_type:
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information. 		1
AgentTypeEnum		 Association manual_agent, automated_agent, computational_model, text_mining_agent
timepoint:
a point in time 		0..1
TimeType		 Association
original_subject:
used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
original_predicate:
used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
Uriorcurie		 Association
original_object:
used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
subject_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Gene
object_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Disease
subject_closure:
Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association
object_closure:
Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['MONDO:0000167', 'MONDO:0005395']
subject_category_closure:
Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Gene", "biolink:NamedThing']
object_category_closure:
Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Disease", "biolink:NamedThing']
subject_namespace:
Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association NCBIGene
object_namespace:
Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association MONDO
subject_label_closure:
Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['BRACA1']
object_label_closure:
Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association breast cancer, cancer
retrieval_source_ids:
A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. 		*
RetrievalSource		 Association
p_value:
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. 		0..1
Float		 Association
adjusted_p_value:
The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<. 		0..1
Float		 Association
has_supporting_studies:
A study that produced information used as evidence to generate the knowledge expressed in an Association. 		*
Study		 Association
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing} 		*
Uriorcurie		 Entity
type:
rdf:type of biolink:Association should be fixed at rdf:Statement 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity
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_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
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

LinkML Source

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)
    range: gene or gene product
  subject aspect qualifier:
    name: subject aspect qualifier
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  object:
    name: object
    range: disease or phenotypic feature
  object direction qualifier:
    name: object direction qualifier
    range: DirectionQualifierEnum
  predicate:
    name: predicate
    subproperty_of: affects