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Class: Pathway (DEPRECATED)

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

URI: nmdc:Pathway

classDiagram class Pathway click Pathway href "../Pathway" FunctionalAnnotationTerm <|-- Pathway click FunctionalAnnotationTerm href "../FunctionalAnnotationTerm" Pathway : alternative_identifiers Pathway : description Pathway : id Pathway : name Pathway : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 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 *
Uriorcurie		 A list of alternative identifiers for the entity NamedThing
type 1
Uriorcurie		 the class_uri of the class that has been instantiated NamedThing

Aliases

  • biological process
  • metabolic pathway
  • signaling pathway

TODOs

  • If we reverted to including Reaction in the schema, then a Reaction would be a reasonable part_of a Pathway
  • is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in the Data Portal?

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

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
deprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881
todos:
- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable
  part_of a Pathway
- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in
  the Data Portal?
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biological process
- metabolic pathway
- signaling pathway
exact_mappings:
- biolink:Pathway
is_a: FunctionalAnnotationTerm
class_uri: nmdc:Pathway

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
deprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881
todos:
- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable
  part_of a Pathway
- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in
  the Data Portal?
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biological process
- metabolic pathway
- signaling pathway
exact_mappings:
- biolink:Pathway
is_a: FunctionalAnnotationTerm
attributes:
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: Pathway
    domain_of:
    - NamedThing
    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:
    - PersonValue
    - NamedThing
    - Protocol
    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:
    - ImageValue
    - NamedThing
    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
    alias: alternative_identifiers
    owner: Pathway
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: Pathway
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:Pathway