Class: MetacycPathways

MetaCyc metabolic pathways with hierarchical classification.

TOTAL PATHWAYS: 1,538

HIERARCHY: - PATHWAYS (root) - Categories (e.g., BIOLUMINESCENCE with 7 instances) - Specific pathways (BACTERIAL, CORAL, DINOFLAGELLATE, etc.)

USAGE: For detailed pathway analysis with reaction-level information. Use pathway_id to join with metacyc_pathway_reactions.

URI: https://w3id.org/kbase/nmdc_core/MetacycPathways

classDiagram class MetacycPathways click MetacycPathways href "../MetacycPathways/" MetacycPathways : description MetacycPathways : name MetacycPathways : parent_pathway MetacycPathways : pathway_id

Slots

Name	Cardinality and Range	Description	Inheritance
pathway_id	1 String	MetaCyc pathway identifier	direct
name	0..1 String	Pathway name	direct
description	0..1 String	Pathway description	direct
parent_pathway	0..1 String	Parent pathway in hierarchy	direct

Identifier and Mapping Information

Annotations

property	value
source_table	metacyc_pathways

Schema Source

from schema: https://w3id.org/kbase/nmdc_core

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/nmdc_core/MetacycPathways
native	https://w3id.org/kbase/nmdc_core/MetacycPathways

LinkML Source

Direct

name: MetacycPathways
annotations:
  source_table:
    tag: source_table
    value: metacyc_pathways
description: 'MetaCyc metabolic pathways with hierarchical classification.

  TOTAL PATHWAYS: 1,538

  HIERARCHY: - PATHWAYS (root) - Categories (e.g., BIOLUMINESCENCE with 7 instances)
  - Specific pathways (BACTERIAL, CORAL, DINOFLAGELLATE, etc.)

  USAGE: For detailed pathway analysis with reaction-level information. Use pathway_id
  to join with metacyc_pathway_reactions.'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  pathway_id:
    name: pathway_id
    description: MetaCyc pathway identifier
    examples:
    - value: PATHWAYS
      description: Root of pathway hierarchy
    - value: BIOLUMINESCENCE
      description: Category with 7 pathway instances
    - value: BACTERIAL
      description: Bacterial bioluminescence pathway
    - value: CORAL
      description: Coral bioluminescence
    from_schema: https://w3id.org/kbase/nmdc_core
    identifier: true
    domain_of:
    - KeggPathwayTerms
    - MetacycPathways
    range: string
    required: true
  name:
    name: name
    description: Pathway name
    examples:
    - value: Pathways
      description: Root name
    - value: (7 instances)
      description: Category with count
    - value: bioluminescence
      description: Specific pathway type
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  description:
    name: description
    description: Pathway description
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - EcTerms
    - CogCategories
    - StudyTable
    - MetacycPathways
    range: string
  parent_pathway:
    name: parent_pathway
    description: Parent pathway in hierarchy
    comments:
    - Self-referential foreign key to MetacycPathways.pathway_id
    examples:
    - value: PATHWAYS
      description: Direct child of root
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - MetacycPathways
    range: string

Induced

name: MetacycPathways
annotations:
  source_table:
    tag: source_table
    value: metacyc_pathways
description: 'MetaCyc metabolic pathways with hierarchical classification.

  TOTAL PATHWAYS: 1,538

  HIERARCHY: - PATHWAYS (root) - Categories (e.g., BIOLUMINESCENCE with 7 instances)
  - Specific pathways (BACTERIAL, CORAL, DINOFLAGELLATE, etc.)

  USAGE: For detailed pathway analysis with reaction-level information. Use pathway_id
  to join with metacyc_pathway_reactions.'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  pathway_id:
    name: pathway_id
    description: MetaCyc pathway identifier
    examples:
    - value: PATHWAYS
      description: Root of pathway hierarchy
    - value: BIOLUMINESCENCE
      description: Category with 7 pathway instances
    - value: BACTERIAL
      description: Bacterial bioluminescence pathway
    - value: CORAL
      description: Coral bioluminescence
    from_schema: https://w3id.org/kbase/nmdc_core
    identifier: true
    alias: pathway_id
    owner: MetacycPathways
    domain_of:
    - KeggPathwayTerms
    - MetacycPathways
    range: string
    required: true
  name:
    name: name
    description: Pathway name
    examples:
    - value: Pathways
      description: Root name
    - value: (7 instances)
      description: Category with count
    - value: bioluminescence
      description: Specific pathway type
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: name
    owner: MetacycPathways
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  description:
    name: description
    description: Pathway description
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: description
    owner: MetacycPathways
    domain_of:
    - AnnotationTermsUnified
    - EcTerms
    - CogCategories
    - StudyTable
    - MetacycPathways
    range: string
  parent_pathway:
    name: parent_pathway
    description: Parent pathway in hierarchy
    comments:
    - Self-referential foreign key to MetacycPathways.pathway_id
    examples:
    - value: PATHWAYS
      description: Direct child of root
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: parent_pathway
    owner: MetacycPathways
    domain_of:
    - MetacycPathways
    range: string