Class: Phenotype

Table containing phenotype information

classDiagram class Phenotype click Phenotype href "../Phenotype" Phenotype : additional_details Phenotype : additional_modifiers Phenotype --> "*" AdditionalModifiersEnum : additional_modifiers click AdditionalModifiersEnum href "../AdditionalModifiersEnum" Phenotype : onset_age_range Phenotype --> "0..1" OnsetAgeRangeEnum : onset_age_range click OnsetAgeRangeEnum href "../OnsetAgeRangeEnum" Phenotype : ontology Phenotype --> "1" OntologyEnum : ontology click OntologyEnum href "../OntologyEnum" Phenotype : participant_id Phenotype : phenotype_id Phenotype : presence Phenotype --> "1" PresenceEnum : presence click PresenceEnum href "../PresenceEnum" Phenotype : syndromic Phenotype --> "0..1" SyndromicEnum : syndromic click SyndromicEnum href "../SyndromicEnum" Phenotype : term_id

Slots

Name	Cardinality and Range	Description	Inheritance
phenotype_id	1 String	primary key	direct
participant_id	1 String		direct
term_id	1 String		direct
presence	1 PresenceEnum		direct
ontology	1 OntologyEnum		direct
additional_details	0..1 String	modifier of a term where the additional details are not supported/available a...	direct
onset_age_range	0..1 OnsetAgeRangeEnum		direct
additional_modifiers	* AdditionalModifiersEnum		direct
syndromic	0..1 SyndromicEnum	For participants with few HPO terms, this optional field is to provide contex...	direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/madanucd/gregor_linkml

Mappings

Mapping Type	Mapped Value
self	gregor_linkml:Phenotype
native	gregor_linkml:Phenotype

LinkML Source

Direct

name: Phenotype
description: Table containing phenotype information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- phenotype_id
- participant_id
- term_id
- presence
- ontology
- additional_details
- onset_age_range
- additional_modifiers
- syndromic

Induced

name: Phenotype
description: Table containing phenotype information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  phenotype_id:
    name: phenotype_id
    description: primary key
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: phenotype_id
    owner: Phenotype
    domain_of:
    - Phenotype
    range: string
    required: true
  participant_id:
    name: participant_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_id
    owner: Phenotype
    domain_of:
    - Participant
    - Phenotype
    - Genetic_findings
    - Analyte
    - Experiment
    - Aligned
    range: string
    required: true
  term_id:
    name: term_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: term_id
    owner: Phenotype
    domain_of:
    - Phenotype
    range: string
    required: true
  presence:
    name: presence
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: presence
    owner: Phenotype
    domain_of:
    - Phenotype
    range: PresenceEnum
    required: true
  ontology:
    name: ontology
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: ontology
    owner: Phenotype
    domain_of:
    - Phenotype
    range: OntologyEnum
    required: true
  additional_details:
    name: additional_details
    description: modifier of a term where the additional details are not supported/available
      as a term in HPO
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: additional_details
    owner: Phenotype
    domain_of:
    - Phenotype
    range: string
  onset_age_range:
    name: onset_age_range
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: onset_age_range
    owner: Phenotype
    domain_of:
    - Phenotype
    range: Onset_age_rangeEnum
  additional_modifiers:
    name: additional_modifiers
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: additional_modifiers
    owner: Phenotype
    domain_of:
    - Phenotype
    range: Additional_modifiersEnum
  syndromic:
    name: syndromic
    description: For participants with few HPO terms, this optional field is to provide
      context on whether it is likely the most notable phenotype or cohort level phenotype
      or whether the individual really only has one trait.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: syndromic
    owner: Phenotype
    domain_of:
    - Phenotype
    range: SyndromicEnum