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Class: DiseaseOrPhenotypicFeature

Description: Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.

Aliases: phenome

classDiagram class DiseaseOrPhenotypicFeature BiologicalEntity <|-- DiseaseOrPhenotypicFeature DiseaseOrPhenotypicFeature <|-- Disease DiseaseOrPhenotypicFeature <|-- PhenotypicFeature DiseaseOrPhenotypicFeature : category DiseaseOrPhenotypicFeature : deprecated DiseaseOrPhenotypicFeature : description DiseaseOrPhenotypicFeature : full_name DiseaseOrPhenotypicFeature : has_attribute DiseaseOrPhenotypicFeature --|> Attribute : has_attribute DiseaseOrPhenotypicFeature : id DiseaseOrPhenotypicFeature : in_taxon DiseaseOrPhenotypicFeature --|> OrganismTaxon : in_taxon DiseaseOrPhenotypicFeature : in_taxon_label DiseaseOrPhenotypicFeature : iri DiseaseOrPhenotypicFeature : name DiseaseOrPhenotypicFeature : provided_by DiseaseOrPhenotypicFeature : synonym DiseaseOrPhenotypicFeature : type DiseaseOrPhenotypicFeature : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
in_taxon:
connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
*
OrganismTaxon		 ThingWithTaxon
in_taxon_label:
The human readable scientific name for the taxon of the entity. 		0..1
LabelType		 ThingWithTaxon
provided_by:
The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph. 		*
String		 NamedThing
xref:
A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references. 		*
Uriorcurie		 NamedThing
full_name:
a long-form human readable name for a thing 		0..1
LabelType		 NamedThing
synonym:
Alternate human-readable names for a thing 		*
LabelType		 NamedThing
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} 		1..*
Uriorcurie		 Entity
type:
None 		*
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

Usages

used by used in type used
GeneExpressionMixin phenotypic_state range DiseaseOrPhenotypicFeature
GeneToGeneCoexpressionAssociation phenotypic_state range DiseaseOrPhenotypicFeature
CellLineToDiseaseOrPhenotypicFeatureAssociation subject range DiseaseOrPhenotypicFeature
CellLineToDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
ChemicalToDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
MaterialSampleToDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
DiseaseOrPhenotypicFeatureToEntityAssociationMixin subject range DiseaseOrPhenotypicFeature
DiseaseOrPhenotypicFeatureToLocationAssociation subject range DiseaseOrPhenotypicFeature
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation subject range DiseaseOrPhenotypicFeature
EntityToDiseaseOrPhenotypicFeatureAssociationMixin object range DiseaseOrPhenotypicFeature
GeneToDiseaseOrPhenotypicFeatureAssociation object range DiseaseOrPhenotypicFeature
VariantToGeneExpressionAssociation phenotypic_state range DiseaseOrPhenotypicFeature

LinkML Source

name: disease or phenotypic feature
description: Either one of a disease or an individual phenotypic feature. Some knowledge
  resources such as Monarch treat these as distinct, others such as MESH conflate.  Please
  see definitions of phenotypic feature and disease in this model for their independent
  descriptions.  This class is helpful to enforce domains and ranges that may involve
  either a disease or a phenotypic feature.
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- phenome
narrow_mappings:
- STY:T033
is_a: biological entity
union_of:
- disease
- phenotypic feature