Class: Pathway

Reactome pathway entity representing a curated biological pathway or reaction-level pathway context relevant to ALS mechanisms, including neuroinflammation, RNA metabolism, protein homeostasis, mitochondrial dysfunction, and axonal transport.

URI: biolink:Pathway

 classDiagram
    class Pathway
    click Pathway href "../Pathway/"
      BiologicalConcept <|-- Pathway
        click BiologicalConcept href "../BiologicalConcept/"

      Pathway : comment

      Pathway : definition

      Pathway : id

      Pathway : ingest_date

      Pathway : is_obsolete

      Pathway : label

      Pathway : last_updated

      Pathway : parent_pathway

      Pathway : pathway_definition

      Pathway : pathway_name

      Pathway : reactome_id

      Pathway : source

      Pathway : source_version

      Pathway : species

      Pathway : synonym

      Pathway : xref

Inheritance

NamedEntity
- OntologyClass
  - BiologicalConcept
    - Pathway

Class Properties

Property	Value
Class URI	biolink:Pathway

Slots

Name	Cardinality and Range	Description	Inheritance
reactome_id	1 ReactomeIdentifier		direct
pathway_name	0..1 String	Standard Reactome pathway name	direct
pathway_definition	0..1 String	Reactome pathway description or summary when available	direct
species	0..1 String	Species for the Reactome pathway; expected to be Homo sapiens for human ALS K...	direct
parent_pathway	* ReactomeIdentifier	Parent Reactome pathway CURIE when available	direct
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
ProteinPathwayAssociation	has_pathway	range	Pathway

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	biolink:Pathway
native	alskb:Pathway

LinkML Source

Direct

name: Pathway
description: Reactome pathway entity representing a curated biological pathway or
  reaction-level pathway context relevant to ALS mechanisms, including neuroinflammation,
  RNA metabolism, protein homeostasis, mitochondrial dysfunction, and axonal transport.
from_schema: https://cair2015.github.io/als-kg
is_a: BiologicalConcept
attributes:
  reactome_id:
    name: reactome_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    domain_of:
    - Pathway
    range: ReactomeIdentifier
    required: true
  pathway_name:
    name: pathway_name
    description: Standard Reactome pathway name
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:name
    domain_of:
    - Pathway
  pathway_definition:
    name: pathway_definition
    description: Reactome pathway description or summary when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: IAO:0000115
    domain_of:
    - Pathway
  species:
    name: species
    description: Species for the Reactome pathway; expected to be Homo sapiens for
      human ALS KG assertions
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Pathway
    - ProteinPathwayAssociation
  parent_pathway:
    name: parent_pathway
    description: Parent Reactome pathway CURIE when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Pathway
    range: ReactomeIdentifier
    multivalued: true
class_uri: biolink:Pathway

Induced

name: Pathway
description: Reactome pathway entity representing a curated biological pathway or
  reaction-level pathway context relevant to ALS mechanisms, including neuroinflammation,
  RNA metabolism, protein homeostasis, mitochondrial dysfunction, and axonal transport.
from_schema: https://cair2015.github.io/als-kg
is_a: BiologicalConcept
attributes:
  reactome_id:
    name: reactome_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    alias: reactome_id
    owner: Pathway
    domain_of:
    - Pathway
    range: ReactomeIdentifier
    required: true
  pathway_name:
    name: pathway_name
    description: Standard Reactome pathway name
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: schema:name
    alias: pathway_name
    owner: Pathway
    domain_of:
    - Pathway
    range: string
  pathway_definition:
    name: pathway_definition
    description: Reactome pathway description or summary when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    slot_uri: IAO:0000115
    alias: pathway_definition
    owner: Pathway
    domain_of:
    - Pathway
    range: string
  species:
    name: species
    description: Species for the Reactome pathway; expected to be Homo sapiens for
      human ALS KG assertions
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: species
    owner: Pathway
    domain_of:
    - Pathway
    - ProteinPathwayAssociation
    range: string
  parent_pathway:
    name: parent_pathway
    description: Parent Reactome pathway CURIE when available
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: parent_pathway
    owner: Pathway
    domain_of:
    - Pathway
    range: ReactomeIdentifier
    multivalued: true
  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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    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: Pathway
    domain_of:
    - NamedEntity
    - Association
    range: string
class_uri: biolink:Pathway