Class: Pathway

A pathway is a sequence of steps/reactions carried out by an organism or community of organisms

classDiagram class Pathway click Pathway href "../Pathway" FunctionalAnnotationTerm <|-- Pathway click FunctionalAnnotationTerm href "../FunctionalAnnotationTerm" Pathway : alternative_identifiers Pathway : description Pathway : has_part Pathway --> "*" Reaction : has_part click Reaction href "../Reaction" Pathway : id Pathway : name

Inheritance

NamedThing
- OntologyClass
  - FunctionalAnnotationTerm
    - Pathway

Slots

Name	Cardinality and Range	Description	Inheritance
has_part	1..* Reaction	A pathway can be broken down to a series of reaction step	direct
id	1..1 Uriorcurie	A unique identifier for a thing	NamedThing
name	0..1 String	A human readable label for an entity	NamedThing
description	0..1 String	a human-readable description of a thing	NamedThing
alternative_identifiers	0..* Uriorcurie	A list of alternative identifiers for the entity	NamedThing

Usages

used by	used in	type	used
Pathway	has_part	domain	Pathway

Aliases

biological process
metabolic pathway
signaling pathway

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

KEGG_PATHWAY
COG

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:Pathway
native	nmdc:Pathway
exact	biolink:Pathway

LinkML Source

Direct

name: Pathway
id_prefixes:
- KEGG_PATHWAY
- COG
description: A pathway is a sequence of steps/reactions carried out by an organism
  or community of organisms
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biological process
- metabolic pathway
- signaling pathway
exact_mappings:
- biolink:Pathway
is_a: FunctionalAnnotationTerm
slots:
- has_part
slot_usage:
  has_part:
    name: has_part
    description: A pathway can be broken down to a series of reaction step
    domain_of:
    - Pathway
    range: Reaction
    required: true

Induced

name: Pathway
id_prefixes:
- KEGG_PATHWAY
- COG
description: A pathway is a sequence of steps/reactions carried out by an organism
  or community of organisms
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biological process
- metabolic pathway
- signaling pathway
exact_mappings:
- biolink:Pathway
is_a: FunctionalAnnotationTerm
slot_usage:
  has_part:
    name: has_part
    description: A pathway can be broken down to a series of reaction step
    domain_of:
    - Pathway
    range: Reaction
    required: true
attributes:
  has_part:
    name: has_part
    description: A pathway can be broken down to a series of reaction step
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: Pathway
    multivalued: true
    alias: has_part
    owner: Pathway
    domain_of:
    - Pathway
    range: Reaction
    required: true
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: Pathway
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: Pathway
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: Pathway
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: Pathway
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$