Class: PhenotypicFeature
Description: A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.
Aliases: sign, symptom, phenotype, trait, endophenotype
classDiagram
class PhenotypicFeature
DiseaseOrPhenotypicFeature <|-- PhenotypicFeature
PhenotypicFeature <|-- BehavioralFeature
PhenotypicFeature <|-- ClinicalFinding
PhenotypicFeature : category
PhenotypicFeature : deprecated
PhenotypicFeature : description
PhenotypicFeature : full_name
PhenotypicFeature : has_attribute
PhenotypicFeature --|> Attribute : has_attribute
PhenotypicFeature : id
PhenotypicFeature : in_taxon
PhenotypicFeature --|> OrganismTaxon : in_taxon
PhenotypicFeature : in_taxon_label
PhenotypicFeature : iri
PhenotypicFeature : name
PhenotypicFeature : provided_by
PhenotypicFeature : synonym
PhenotypicFeature : type
PhenotypicFeature : xref
Inheritance
- Entity
- NamedThing
- BiologicalEntity [ ThingWithTaxon]
- DiseaseOrPhenotypicFeature
- PhenotypicFeature
- DiseaseOrPhenotypicFeature
- BiologicalEntity [ ThingWithTaxon]
- NamedThing
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
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
Example values
| Slot Name | Value |
|---|---|
| PhenotypicFeature | MP:0001262 |
LinkML Source
name: phenotypic feature
id_prefixes:
- HP
- EFO
- NCIT
- UMLS
- MEDDRA
- MP
- ZP
- UPHENO
- APO
- FBcv
- WBPhenotype
- SNOMEDCT
- MESH
- XPO
- FYPO
- TO
description: A combination of entity and quality that makes up a phenotyping statement.
An observable characteristic of an individual resulting from the interaction of
its genotype with its molecular and physical environment.
examples:
- value: MP:0001262
description: decreased body weight
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- sign
- symptom
- phenotype
- trait
- endophenotype
exact_mappings:
- UPHENO:0001001
- SIO:010056
- WIKIDATA:Q104053
- UMLS:C4021819
- NCIT:C16977
- SNOMEDCT:8116006
- MESH:D010641
narrow_mappings:
- STY:T184
- WIKIDATA:Q169872
- WIKIDATA:Q25203551
- ZP:00000000
- FBcv:0001347
- HP:0000118
- MP:0000001
- WBPhenotype:0000886
- XPO:00000000
- FYPO:0000001
- APO:0000017
- TO:0000387
- STY:T190
broad_mappings:
- BFO:0000019
- PATO:0000001
is_a: disease or phenotypic feature