Skip to content

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 : has_input Activity --> "*" MoleculeAssociation : has_input click MoleculeAssociation href "../MoleculeAssociation" Activity : has_output Activity --> "*" MoleculeAssociation : has_output click MoleculeAssociation href "../MoleculeAssociation" Activity : has_primary_input Activity --> "0..1" MoleculeAssociation : has_primary_input click MoleculeAssociation href "../MoleculeAssociation" Activity : has_primary_output Activity --> "0..1" MoleculeAssociation : has_primary_output click MoleculeAssociation href "../MoleculeAssociation" Activity : id 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
has_input *
MoleculeAssociation		 The input molecules that are directly consumed by the activity direct
has_primary_input 0..1
MoleculeAssociation		 The primary input molecule that is directly consumed by the activity direct
has_output *
MoleculeAssociation		 The output molecules that are directly produced by the activity direct
has_primary_output 0..1
MoleculeAssociation		 The primary output molecule that is directly produced by the activity 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:
    - gocam
    description: Identifier of the activity unit. Should be in gocam namespace.
    comments:
    - Typically does not need to be exposed to end-user, this exists to allow activity
      flows
    examples:
    - value: gomodel:63f809ec00000701
      description: A model representing tRNA repair and recycling
    from_schema: https://w3id.org/gocam
    identifier: true
    domain_of:
    - Model
    - Activity
    - 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
    rank: 1000
    domain_of:
    - Activity
    - BiologicalProcessAssociation
    - CellularAnatomicalEntityAssociation
    - CellTypeAssociation
    - GrossAnatomyAssociation
    range: BiologicalProcessAssociation
    recommended: true
    inlined: true
  has_input:
    name: has_input
    description: The input molecules that are directly consumed by the activity
    todos:
    - resolve has_input vs has_primary_input
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_primary_input:
    name: has_primary_input
    description: The primary input molecule that is directly consumed by the activity
    todos:
    - resolve has_input vs has_primary_input
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MoleculeAssociation
    inlined: true
  has_output:
    name: has_output
    description: The output molecules that are directly produced by the activity
    todos:
    - resolve has_output vs has_primary_output
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_primary_output:
    name: has_primary_output
    description: The primary output molecule that is directly produced by the activity
    todos:
    - resolve has_output vs has_primary_output
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Activity
    range: MoleculeAssociation
    inlined: 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:
    - gocam
    description: Identifier of the activity unit. Should be in gocam namespace.
    comments:
    - Typically does not need to be exposed to end-user, this exists to allow activity
      flows
    examples:
    - value: gomodel:63f809ec00000701
      description: A model representing tRNA repair and recycling
    from_schema: https://w3id.org/gocam
    identifier: true
    alias: id
    owner: Activity
    domain_of:
    - Model
    - Activity
    - 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
    rank: 1000
    alias: part_of
    owner: Activity
    domain_of:
    - Activity
    - BiologicalProcessAssociation
    - CellularAnatomicalEntityAssociation
    - CellTypeAssociation
    - GrossAnatomyAssociation
    range: BiologicalProcessAssociation
    recommended: true
    inlined: true
  has_input:
    name: has_input
    description: The input molecules that are directly consumed by the activity
    todos:
    - resolve has_input vs has_primary_input
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: has_input
    owner: Activity
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_primary_input:
    name: has_primary_input
    description: The primary input molecule that is directly consumed by the activity
    todos:
    - resolve has_input vs has_primary_input
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: has_primary_input
    owner: Activity
    domain_of:
    - Activity
    range: MoleculeAssociation
    inlined: true
  has_output:
    name: has_output
    description: The output molecules that are directly produced by the activity
    todos:
    - resolve has_output vs has_primary_output
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: has_output
    owner: Activity
    domain_of:
    - Activity
    range: MoleculeAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_primary_output:
    name: has_primary_output
    description: The primary output molecule that is directly produced by the activity
    todos:
    - resolve has_output vs has_primary_output
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: has_primary_output
    owner: Activity
    domain_of:
    - Activity
    range: MoleculeAssociation
    inlined: 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