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Class: Phenotype

Phenotypic feature (HPO term). Represents observable/measurable characteristics associated with diseases. Distinct from drug side effects which are modeled via DrugCausesPhenotype relationships.

URI: biolink:PhenotypicFeature

 classDiagram
    class Phenotype
    click Phenotype href "../Phenotype/"
      DiseaseOrPhenotype <|-- Phenotype
        click DiseaseOrPhenotype href "../DiseaseOrPhenotype/"

      Phenotype : comment

      Phenotype : definition

      Phenotype : frequency

      Phenotype : hpo_id

      Phenotype : id

      Phenotype : ingest_date

      Phenotype : is_obsolete

      Phenotype : label

      Phenotype : last_updated

      Phenotype : mondo_id

      Phenotype : severity

      Phenotype : source

      Phenotype : source_version

      Phenotype : synonym

      Phenotype : xref

Inheritance

Class Properties

Property Value
Class URI biolink:PhenotypicFeature

Slots

Name Cardinality and Range Description Inheritance
hpo_id 1
HpoIdentifier		 direct
frequency 0..1
String		 Frequency of phenotype in affected individuals (e direct
severity 0..1
String		 Severity scale direct
mondo_id 0..1
MondoIdentifier		 MONDO cross-reference DiseaseOrPhenotype
source_version 0..1
String		 Source database/ontology version OntologyClass
ingest_date 0..1
String		 When entity was imported into ALS-KG OntologyClass
id 1
String		 Persistent unique identifier (IRI) NamedEntity
label 1
String		 Preferred human-readable label NamedEntity
definition 0..1
String		 Formal textual definition NamedEntity
synonym 0..1
String		 Alternative names NamedEntity
xref 0..1
String		 Cross-references to external ontologies NamedEntity
comment 0..1
String		 Informal notes or comments NamedEntity
is_obsolete 0..1
String		 Deprecation flag NamedEntity
source 0..1
String		 Original source/database NamedEntity
last_updated 0..1
String		 Last modification timestamp NamedEntity

Usages

used by used in type used
DiseasePhenotypeAssociation has_phenotype range Phenotype

Identifier and Mapping Information

Schema Source

  • from schema: https://cair2015.github.io/als-kg

Mappings

Mapping Type Mapped Value
self biolink:PhenotypicFeature
native alskb:Phenotype

LinkML Source

Direct

name: Phenotype
description: Phenotypic feature (HPO term). Represents observable/measurable characteristics
  associated with diseases. Distinct from drug side effects which are modeled via
  DrugCausesPhenotype relationships.
from_schema: https://cair2015.github.io/als-kg
is_a: DiseaseOrPhenotype
attributes:
  hpo_id:
    name: hpo_id
    from_schema: https://cair2015.github.io/als-kg
    identifier: true
    domain_of:
    - DiseaseOrPhenotype
    - Phenotype
    range: HpoIdentifier
    required: true
  frequency:
    name: frequency
    description: Frequency of phenotype in affected individuals (e.g. Frequent 75-99%)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
  severity:
    name: severity
    description: Severity scale
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
class_uri: biolink:PhenotypicFeature

Induced

name: Phenotype
description: Phenotypic feature (HPO term). Represents observable/measurable characteristics
  associated with diseases. Distinct from drug side effects which are modeled via
  DrugCausesPhenotype relationships.
from_schema: https://cair2015.github.io/als-kg
is_a: DiseaseOrPhenotype
attributes:
  hpo_id:
    name: hpo_id
    from_schema: https://cair2015.github.io/als-kg
    identifier: true
    alias: hpo_id
    owner: Phenotype
    domain_of:
    - DiseaseOrPhenotype
    - Phenotype
    range: HpoIdentifier
    required: true
  frequency:
    name: frequency
    description: Frequency of phenotype in affected individuals (e.g. Frequent 75-99%)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: frequency
    owner: Phenotype
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
  severity:
    name: severity
    description: Severity scale
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: severity
    owner: Phenotype
    domain_of:
    - Phenotype
    - DiseasePhenotypeAssociation
    range: string
  mondo_id:
    name: mondo_id
    description: MONDO cross-reference
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: mondo_id
    owner: Phenotype
    domain_of:
    - DiseaseOrPhenotype
    - Disease
    range: MondoIdentifier
  source_version:
    name: source_version
    description: Source database/ontology version
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:hasVersion
    alias: source_version
    owner: Phenotype
    domain_of:
    - OntologyClass
    - Association
    range: string
  ingest_date:
    name: ingest_date
    description: When entity was imported into ALS-KG
    from_schema: https://cair2015.github.io/als-kg
    alias: ingest_date
    owner: Phenotype
    domain_of:
    - OntologyClass
    - Relationship
    - Association
    range: string
  id:
    name: id
    description: Persistent unique identifier (IRI)
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: schema:identifier
    alias: id
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
    required: true
  label:
    name: label
    description: Preferred human-readable label
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:label
    alias: label
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
    required: true
  definition:
    name: definition
    description: Formal textual definition
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: IAO:0000115
    alias: definition
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
  synonym:
    name: synonym
    description: Alternative names
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasRelatedSynonym
    alias: synonym
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
  xref:
    name: xref
    description: Cross-references to external ontologies
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasDbXref
    alias: xref
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
  comment:
    name: comment
    description: Informal notes or comments
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:comment
    alias: comment
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
  is_obsolete:
    name: is_obsolete
    description: Deprecation flag
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: owl:deprecated
    ifabsent: 'false'
    alias: is_obsolete
    owner: Phenotype
    domain_of:
    - NamedEntity
    range: string
  source:
    name: source
    description: Original source/database
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:source
    alias: source
    owner: Phenotype
    domain_of:
    - NamedEntity
    - Relationship
    - Association
    range: string
  last_updated:
    name: last_updated
    description: Last modification timestamp
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:modified
    alias: last_updated
    owner: Phenotype
    domain_of:
    - NamedEntity
    - Association
    range: string
class_uri: biolink:PhenotypicFeature