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Class: QueryIndex

An index that is optionally placed on a model in order to support common query or index operations. Note that this index is not typically populated in the working transactional store for a model, it is derived via computation from core primary model information.

URI: gocam:QueryIndex

classDiagram class QueryIndex click QueryIndex href "../QueryIndex" QueryIndex : annoton_terms QueryIndex --> "*" TermObject : annoton_terms click TermObject href "../TermObject" QueryIndex : end_activities QueryIndex --> "*" Activity : end_activities click Activity href "../Activity" QueryIndex : flattened_references QueryIndex --> "*" PublicationObject : flattened_references click PublicationObject href "../PublicationObject" QueryIndex : intermediate_activities QueryIndex --> "*" Activity : intermediate_activities click Activity href "../Activity" QueryIndex : length_of_longest_causal_association_path QueryIndex : model_activity_has_input_closure QueryIndex --> "*" TermObject : model_activity_has_input_closure click TermObject href "../TermObject" QueryIndex : model_activity_has_input_terms QueryIndex --> "*" TermObject : model_activity_has_input_terms click TermObject href "../TermObject" QueryIndex : model_activity_molecular_function_closure QueryIndex --> "*" TermObject : model_activity_molecular_function_closure click TermObject href "../TermObject" QueryIndex : model_activity_molecular_function_terms QueryIndex --> "*" TermObject : model_activity_molecular_function_terms click TermObject href "../TermObject" QueryIndex : model_activity_occurs_in_closure QueryIndex --> "*" TermObject : model_activity_occurs_in_closure click TermObject href "../TermObject" QueryIndex : model_activity_occurs_in_terms QueryIndex --> "*" TermObject : model_activity_occurs_in_terms click TermObject href "../TermObject" QueryIndex : model_activity_part_of_closure QueryIndex --> "*" TermObject : model_activity_part_of_closure click TermObject href "../TermObject" QueryIndex : model_activity_part_of_terms QueryIndex --> "*" TermObject : model_activity_part_of_terms click TermObject href "../TermObject" QueryIndex : number_of_activities QueryIndex : number_of_causal_associations QueryIndex : number_of_enabled_by_terms QueryIndex : number_of_end_activities QueryIndex : number_of_intermediate_activities QueryIndex : number_of_singleton_activities QueryIndex : number_of_start_activities QueryIndex : number_of_strongly_connected_components QueryIndex : singleton_activities QueryIndex --> "*" Activity : singleton_activities click Activity href "../Activity" QueryIndex : start_activities QueryIndex --> "*" Activity : start_activities click Activity href "../Activity" QueryIndex : taxon_closure QueryIndex --> "*" TermObject : taxon_closure click TermObject href "../TermObject"

Slots

Name Cardinality and Range Description Inheritance
number_of_activities 0..1
Integer		 The number of activities in a model direct
number_of_enabled_by_terms 0..1
Integer		 The number of molecular entities or sets of entities in a model direct
number_of_causal_associations 0..1
Integer		 Total number of causal association edges connecting activities in a model direct
length_of_longest_causal_association_path 0..1
Integer		 The maximum number of hops along activities along the direction of causal flo... direct
number_of_strongly_connected_components 0..1
Integer		 The number of distinct components that consist of activities that are connect... direct
flattened_references *
PublicationObject		 All publication objects from the model across different levels combined in on... direct
model_activity_molecular_function_terms *
TermObject		 All MF terms for all activities direct
model_activity_molecular_function_closure *
TermObject		 The reflexive transitive closure of model_activity_molecular_function_terms... direct
model_activity_occurs_in_terms *
TermObject		 direct
model_activity_occurs_in_closure *
TermObject		 direct
model_activity_part_of_terms *
TermObject		 direct
model_activity_part_of_closure *
TermObject		 direct
model_activity_has_input_terms *
TermObject		 direct
model_activity_has_input_closure *
TermObject		 direct
taxon_closure *
TermObject		 direct
annoton_terms *
TermObject		 direct
start_activities *
Activity		 direct
end_activities *
Activity		 direct
intermediate_activities *
Activity		 direct
singleton_activities *
Activity		 direct
number_of_start_activities 0..1
Integer		 The number of start activities in a model direct
number_of_end_activities 0..1
Integer		 The number of end activities in a model direct
number_of_intermediate_activities 0..1
Integer		 The number of intermediate activities in a model direct
number_of_singleton_activities 0..1
Integer		 The number of singleton activities in a model direct

Usages

used by used in type used
Model query_index range QueryIndex

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: QueryIndex
description: An index that is optionally placed on a model in order to support common
  query or index operations. Note that this index is not typically populated in the
  working transactional store for a model, it is derived via computation from core
  primary model information.
from_schema: https://w3id.org/gocam
attributes:
  number_of_activities:
    name: number_of_activities
    description: The number of activities in a model.
    comments:
    - this includes all activities, even those without an enabler.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_enabled_by_terms:
    name: number_of_enabled_by_terms
    description: The number of molecular entities or sets of entities in a model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_causal_associations:
    name: number_of_causal_associations
    description: Total number of causal association edges connecting activities in
      a model.
    todos:
    - decide what to do about "implicit" causal associations, i.e provides_input_for
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  length_of_longest_causal_association_path:
    name: length_of_longest_causal_association_path
    description: The maximum number of hops along activities along the direction of
      causal flow in a model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_strongly_connected_components:
    name: number_of_strongly_connected_components
    description: The number of distinct components that consist of activities that
      are connected (directly or indirectly) via causal connections. Most models will
      consist of a single SCC. Some models may consist of two or more "islands" where
      there is no connection from one island to another.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  flattened_references:
    name: flattened_references
    description: All publication objects from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: PublicationObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_molecular_function_terms:
    name: model_activity_molecular_function_terms
    description: All MF terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_molecular_function_closure:
    name: model_activity_molecular_function_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    description: The reflexive transitive closure of `model_activity_molecular_function_terms`,
      over the is_a relationship
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_occurs_in_terms:
    name: model_activity_occurs_in_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_occurs_in_closure:
    name: model_activity_occurs_in_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_part_of_terms:
    name: model_activity_part_of_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_part_of_closure:
    name: model_activity_part_of_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_has_input_terms:
    name: model_activity_has_input_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_has_input_closure:
    name: model_activity_has_input_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  taxon_closure:
    name: taxon_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  annoton_terms:
    name: annoton_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  start_activities:
    name: start_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  end_activities:
    name: end_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  intermediate_activities:
    name: intermediate_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  singleton_activities:
    name: singleton_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  number_of_start_activities:
    name: number_of_start_activities
    description: The number of start activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_end_activities:
    name: number_of_end_activities
    description: The number of end activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_intermediate_activities:
    name: number_of_intermediate_activities
    description: The number of intermediate activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer
  number_of_singleton_activities:
    name: number_of_singleton_activities
    description: The number of singleton activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: integer

Induced

name: QueryIndex
description: An index that is optionally placed on a model in order to support common
  query or index operations. Note that this index is not typically populated in the
  working transactional store for a model, it is derived via computation from core
  primary model information.
from_schema: https://w3id.org/gocam
attributes:
  number_of_activities:
    name: number_of_activities
    description: The number of activities in a model.
    comments:
    - this includes all activities, even those without an enabler.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_enabled_by_terms:
    name: number_of_enabled_by_terms
    description: The number of molecular entities or sets of entities in a model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_enabled_by_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_causal_associations:
    name: number_of_causal_associations
    description: Total number of causal association edges connecting activities in
      a model.
    todos:
    - decide what to do about "implicit" causal associations, i.e provides_input_for
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_causal_associations
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  length_of_longest_causal_association_path:
    name: length_of_longest_causal_association_path
    description: The maximum number of hops along activities along the direction of
      causal flow in a model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: length_of_longest_causal_association_path
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_strongly_connected_components:
    name: number_of_strongly_connected_components
    description: The number of distinct components that consist of activities that
      are connected (directly or indirectly) via causal connections. Most models will
      consist of a single SCC. Some models may consist of two or more "islands" where
      there is no connection from one island to another.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_strongly_connected_components
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  flattened_references:
    name: flattened_references
    description: All publication objects from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: flattened_references
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: PublicationObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_molecular_function_terms:
    name: model_activity_molecular_function_terms
    description: All MF terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_molecular_function_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_molecular_function_closure:
    name: model_activity_molecular_function_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    description: The reflexive transitive closure of `model_activity_molecular_function_terms`,
      over the is_a relationship
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_molecular_function_closure
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_occurs_in_terms:
    name: model_activity_occurs_in_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_occurs_in_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_occurs_in_closure:
    name: model_activity_occurs_in_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_occurs_in_closure
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_part_of_terms:
    name: model_activity_part_of_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_part_of_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_part_of_closure:
    name: model_activity_part_of_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_part_of_closure
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_has_input_terms:
    name: model_activity_has_input_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_has_input_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_has_input_closure:
    name: model_activity_has_input_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: model_activity_has_input_closure
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  taxon_closure:
    name: taxon_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: taxon_closure
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  annoton_terms:
    name: annoton_terms
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: annoton_terms
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  start_activities:
    name: start_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: start_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  end_activities:
    name: end_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: end_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  intermediate_activities:
    name: intermediate_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: intermediate_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  singleton_activities:
    name: singleton_activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: singleton_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  number_of_start_activities:
    name: number_of_start_activities
    description: The number of start activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_start_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_end_activities:
    name: number_of_end_activities
    description: The number of end activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_end_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_intermediate_activities:
    name: number_of_intermediate_activities
    description: The number of intermediate activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_intermediate_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer
  number_of_singleton_activities:
    name: number_of_singleton_activities
    description: The number of singleton activities in a model
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: number_of_singleton_activities
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer