Class: Pathway (DEPRECATED)

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 : alternative_names Pathway : definition Pathway : description Pathway : id Pathway : is_obsolete Pathway : is_root Pathway : name Pathway : relations Pathway --> "*" OntologyRelation : relations click OntologyRelation href "../OntologyRelation" Pathway : type

Inheritance

NamedThing
- OntologyClass
  - FunctionalAnnotationTerm
    - Pathway

Slots

Name	Cardinality and Range	Description	Inheritance
alternative_names	* String	A list of alternative names used to refer to the entity	OntologyClass
relations	* OntologyRelation		OntologyClass
definition	0..1 String	The definition of the ontology term as provided by the ontology	OntologyClass
is_obsolete	0..1 Boolean	A boolean value indicating whether the ontology term is obsolete	OntologyClass
is_root	0..1 Boolean	A boolean value indicating whether the ontology term is a root term; it is no...	OntologyClass
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

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
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:
  alternative_names:
    name: alternative_names
    description: A list of alternative names used to refer to the entity. The distinction
      between name and alternative names is application-specific.
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - dcterms:alternative
    - skos:altLabel
    rank: 1000
    alias: alternative_names
    owner: Pathway
    domain_of:
    - OntologyClass
    - Study
    range: string
    multivalued: true
  relations:
    name: relations
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: relations
    owner: Pathway
    domain_of:
    - OntologyClass
    range: OntologyRelation
    multivalued: true
    inlined: true
    inlined_as_list: true
  definition:
    name: definition
    description: The definition of the ontology term as provided by the ontology.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: definition
    owner: Pathway
    domain_of:
    - OntologyClass
    range: string
  is_obsolete:
    name: is_obsolete
    description: A boolean value indicating whether the ontology term is obsolete.
    comments:
    - If true (the ontology term is declared obsolete via the ontology source itself),  the
      term is no longer considered a valid term to use in an annotation at NMDC, and
      it no longer has ontology_relation_set records.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_obsolete
    owner: Pathway
    domain_of:
    - OntologyClass
    range: boolean
  is_root:
    name: is_root
    description: A boolean value indicating whether the ontology term is a root term;
      it is not a subclass of  any other term.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: is_root
    owner: Pathway
    domain_of:
    - OntologyClass
    range: boolean
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    notes:
    - The identifiers for terms from external ontologies can't have their ids constrained
      to the nmdc namespace
    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
    structured_aliases:
      workflow_execution_id:
        literal_form: workflow_execution_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
      data_object_id:
        literal_form: data_object_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    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:
    - 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
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: Pathway
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:Pathway