Class: Activity

An individual activity in a causal model, representing the individual molecular activity of a single gene product or complex in the context of a particular model

URI: gocam:Activity

classDiagram class Activity click Activity href "../Activity/" Activity : causal_associations Activity --> "*" CausalAssociation : causal_associations click CausalAssociation href "../CausalAssociation/" Activity : enabled_by Activity --> "0..1 _recommended_" EnabledByAssociation : enabled_by click EnabledByAssociation href "../EnabledByAssociation/" Activity : happens_during Activity --> "0..1" PhaseAssociation : happens_during click PhaseAssociation href "../PhaseAssociation/" Activity : id Activity : molecular_associations Activity --> "*" MoleculeAssociation : molecular_associations click MoleculeAssociation href "../MoleculeAssociation/" Activity : molecular_function Activity --> "0..1 _recommended_" MolecularFunctionAssociation : molecular_function click MolecularFunctionAssociation href "../MolecularFunctionAssociation/" Activity : occurs_in Activity --> "0..1 _recommended_" CellularAnatomicalEntityAssociation : occurs_in click CellularAnatomicalEntityAssociation href "../CellularAnatomicalEntityAssociation/" Activity : part_of Activity --> "0..1 _recommended_" BiologicalProcessAssociation : part_of click BiologicalProcessAssociation href "../BiologicalProcessAssociation/" Activity : provenances Activity --> "*" ProvenanceInfo : provenances click ProvenanceInfo href "../ProvenanceInfo/"

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 Uriorcurie	Identifier of the activity unit	direct
enabled_by	0..1 recommended EnabledByAssociation	The gene product or complex that carries out the activity	direct
molecular_function	0..1 recommended MolecularFunctionAssociation	The molecular function that is carried out by the gene product or complex	direct
occurs_in	0..1 recommended CellularAnatomicalEntityAssociation	The cellular location in which the activity occurs	direct
part_of	0..1 recommended BiologicalProcessAssociation	The larger biological process in which the activity is a part	direct
happens_during	0..1 PhaseAssociation	The phase during which the activity takes place	direct
molecular_associations	* MoleculeAssociation	Associations between the activity and molecules that are relevant to it	direct
causal_associations	* CausalAssociation	The causal associations that flow out of this activity	direct
provenances	* ProvenanceInfo	Provenance information for the activity	direct

Usages

used by	used in	type	used
Model	activities	range	Activity
CausalAssociation	downstream_activity	range	Activity
QueryIndex	start_activities	range	Activity
QueryIndex	end_activities	range	Activity
QueryIndex	intermediate_activities	range	Activity
QueryIndex	singleton_activities	range	Activity

Aliases

annoton

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	gocam:Activity
native	gocam:Activity

LinkML Source

Direct

name: Activity
description: An individual activity in a causal model, representing the individual
  molecular activity of a single gene product or complex in the context of a particular
  model
from_schema: https://w3id.org/gocam
aliases:
- annoton
attributes:
  id:
    name: id
    id_prefixes:
    - gomodel
    description: Identifier of the activity unit.
    comments:
    - Typically does not need to be exposed to end-user, this exists to allow activity
      flows
    examples:
    - value: gomodel:63f809ec00000701/63f809ec00000706
      description: A activity of the model representing alpha-aminoacyl-tRNA binding
        enabled by NEMF
    from_schema: https://w3id.org/gocam
    identifier: true
    domain_of:
    - Model
    - Activity
    - MoleculeNode
    - Object
    range: uriorcurie
    required: true
  enabled_by:
    name: enabled_by
    description: The gene product or complex that carries out the activity
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: EnabledByAssociation
    recommended: true
    inlined: true
  molecular_function:
    name: molecular_function
    description: The molecular function that is carried out by the gene product or
      complex
    todos:
    - currently BP, CC etc are at the level of the activity, not the MolecularFunctionAssociation
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MolecularFunctionAssociation
    recommended: true
    inlined: true
  occurs_in:
    name: occurs_in
    description: The cellular location in which the activity occurs
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: CellularAnatomicalEntityAssociation
    recommended: true
    inlined: true
  part_of:
    name: part_of
    description: The larger biological process in which the activity is a part
    from_schema: https://w3id.org/gocam
    domain_of:
    - Activity
    - EnabledByGeneProductAssociation
    - ProteinComplexHasPartAssociation
    - BiologicalProcessAssociation
    - CellularAnatomicalEntityAssociation
    - CellTypeAssociation
    - GrossAnatomyAssociation
    range: BiologicalProcessAssociation
    recommended: true
    inlined: true
  happens_during:
    name: happens_during
    description: The phase during which the activity takes place
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    - BiologicalProcessAssociation
    range: PhaseAssociation
    inlined: true
  molecular_associations:
    name: molecular_associations
    description: Associations between the activity and molecules that are relevant
      to it. This includes molecules that are products/substrates or regulators of
      the activity.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  causal_associations:
    name: causal_associations
    description: The causal associations that flow out of this activity
    comments:
    - All activities in a model must be connected to at least one other activity.
      If a an activity has no outgoing activities (i.e the value of this slot is empty)
      then it is a terminal activity in the model. If an activity has no incoming
      activities, it is an initial activity.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: CausalAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  provenances:
    name: provenances
    description: Provenance information for the activity
    from_schema: https://w3id.org/gocam
    domain_of:
    - Model
    - Activity
    - EvidenceItem
    - Association
    range: ProvenanceInfo
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: Activity
description: An individual activity in a causal model, representing the individual
  molecular activity of a single gene product or complex in the context of a particular
  model
from_schema: https://w3id.org/gocam
aliases:
- annoton
attributes:
  id:
    name: id
    id_prefixes:
    - gomodel
    description: Identifier of the activity unit.
    comments:
    - Typically does not need to be exposed to end-user, this exists to allow activity
      flows
    examples:
    - value: gomodel:63f809ec00000701/63f809ec00000706
      description: A activity of the model representing alpha-aminoacyl-tRNA binding
        enabled by NEMF
    from_schema: https://w3id.org/gocam
    identifier: true
    alias: id
    owner: Activity
    domain_of:
    - Model
    - Activity
    - MoleculeNode
    - Object
    range: uriorcurie
    required: true
  enabled_by:
    name: enabled_by
    description: The gene product or complex that carries out the activity
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: enabled_by
    owner: Activity
    domain_of:
    - Activity
    range: EnabledByAssociation
    recommended: true
    inlined: true
  molecular_function:
    name: molecular_function
    description: The molecular function that is carried out by the gene product or
      complex
    todos:
    - currently BP, CC etc are at the level of the activity, not the MolecularFunctionAssociation
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: molecular_function
    owner: Activity
    domain_of:
    - Activity
    range: MolecularFunctionAssociation
    recommended: true
    inlined: true
  occurs_in:
    name: occurs_in
    description: The cellular location in which the activity occurs
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: occurs_in
    owner: Activity
    domain_of:
    - Activity
    range: CellularAnatomicalEntityAssociation
    recommended: true
    inlined: true
  part_of:
    name: part_of
    description: The larger biological process in which the activity is a part
    from_schema: https://w3id.org/gocam
    alias: part_of
    owner: Activity
    domain_of:
    - Activity
    - EnabledByGeneProductAssociation
    - ProteinComplexHasPartAssociation
    - BiologicalProcessAssociation
    - CellularAnatomicalEntityAssociation
    - CellTypeAssociation
    - GrossAnatomyAssociation
    range: BiologicalProcessAssociation
    recommended: true
    inlined: true
  happens_during:
    name: happens_during
    description: The phase during which the activity takes place
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: happens_during
    owner: Activity
    domain_of:
    - Activity
    - BiologicalProcessAssociation
    range: PhaseAssociation
    inlined: true
  molecular_associations:
    name: molecular_associations
    description: Associations between the activity and molecules that are relevant
      to it. This includes molecules that are products/substrates or regulators of
      the activity.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: molecular_associations
    owner: Activity
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  causal_associations:
    name: causal_associations
    description: The causal associations that flow out of this activity
    comments:
    - All activities in a model must be connected to at least one other activity.
      If a an activity has no outgoing activities (i.e the value of this slot is empty)
      then it is a terminal activity in the model. If an activity has no incoming
      activities, it is an initial activity.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: causal_associations
    owner: Activity
    domain_of:
    - Activity
    range: CausalAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  provenances:
    name: provenances
    description: Provenance information for the activity
    from_schema: https://w3id.org/gocam
    alias: provenances
    owner: Activity
    domain_of:
    - Model
    - Activity
    - EvidenceItem
    - Association
    range: ProvenanceInfo
    multivalued: true
    inlined: true
    inlined_as_list: true