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Class: Pathway

A biological pathway with activity and enrichment information.

URI: namo:Pathway

classDiagram class Pathway click Pathway href "../Pathway/" NamedThing <|-- Pathway click NamedThing href "../NamedThing/" Pathway : activity_score Pathway : description Pathway : enrichment_score Pathway : id Pathway : name Pathway : pathway_database Pathway : pathway_id Pathway : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
pathway_database 0..1
String		 Source database (e direct
pathway_id 0..1
String		 Database-specific pathway identifier direct
activity_score 0..1
Float		 Quantitative measure of pathway activity direct
enrichment_score 0..1
Float		 Statistical enrichment score for the pathway direct
id 1
Uriorcurie		 A unique identifier for a thing NamedThing
name 0..1
String		 A human-readable name for a thing NamedThing
description 0..1
String		 A human-readable description for a thing NamedThing
type 0..1
String		 NamedThing

Usages

used by used in type used
PathwayConcordance active_pathways range Pathway
PathwayConcordance divergent_pathways range Pathway

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/namo

Mappings

Mapping Type Mapped Value
self namo:Pathway
native namo:Pathway

LinkML Source

Direct

name: Pathway
description: A biological pathway with activity and enrichment information.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NamedThing
attributes:
  pathway_database:
    name: pathway_database
    description: Source database (e.g., KEGG, Reactome, GO).
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Pathway
  pathway_id:
    name: pathway_id
    description: Database-specific pathway identifier.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Pathway
  activity_score:
    name: activity_score
    description: Quantitative measure of pathway activity.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Pathway
    range: float
  enrichment_score:
    name: enrichment_score
    description: Statistical enrichment score for the pathway.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Pathway
    - EnrichmentStatistics
    range: float

Induced

name: Pathway
description: A biological pathway with activity and enrichment information.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NamedThing
attributes:
  pathway_database:
    name: pathway_database
    description: Source database (e.g., KEGG, Reactome, GO).
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: pathway_database
    owner: Pathway
    domain_of:
    - Pathway
    range: string
  pathway_id:
    name: pathway_id
    description: Database-specific pathway identifier.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: pathway_id
    owner: Pathway
    domain_of:
    - Pathway
    range: string
  activity_score:
    name: activity_score
    description: Quantitative measure of pathway activity.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: activity_score
    owner: Pathway
    domain_of:
    - Pathway
    range: float
  enrichment_score:
    name: enrichment_score
    description: Statistical enrichment score for the pathway.
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: enrichment_score
    owner: Pathway
    domain_of:
    - Pathway
    - EnrichmentStatistics
    range: float
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: Pathway
    domain_of:
    - NamedThing
    - Reference
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Pathway
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A human-readable description for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Pathway
    domain_of:
    - NamedThing
    range: string
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    designates_type: true
    alias: type
    owner: Pathway
    domain_of:
    - NamedThing
    range: string