Skip to content

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](https://w3id.org/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_contributors QueryIndex : flattened_evidence_terms QueryIndex --> "*" EvidenceTermObject : flattened_evidence_terms click EvidenceTermObject href "../EvidenceTermObject/" QueryIndex : flattened_provided_by QueryIndex --> "*" Object : flattened_provided_by click Object href "../Object/" 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_enabled_by_closure QueryIndex --> "*" TermObject : model_activity_enabled_by_closure click TermObject href "../TermObject/" QueryIndex : model_activity_enabled_by_genes QueryIndex --> "*" TermObject : model_activity_enabled_by_genes click TermObject href "../TermObject/" QueryIndex : model_activity_enabled_by_rollup QueryIndex --> "*" TermObject : model_activity_enabled_by_rollup click TermObject href "../TermObject/" QueryIndex : model_activity_enabled_by_terms QueryIndex --> "*" TermObject : model_activity_enabled_by_terms click TermObject href "../TermObject/" QueryIndex : model_activity_has_input_closure QueryIndex --> "*" TermObject : model_activity_has_input_closure click TermObject href "../TermObject/" QueryIndex : model_activity_has_input_rollup QueryIndex --> "*" TermObject : model_activity_has_input_rollup 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_rollup QueryIndex --> "*" TermObject : model_activity_molecular_function_rollup 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_rollup QueryIndex --> "*" TermObject : model_activity_occurs_in_rollup 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_rollup QueryIndex --> "*" TermObject : model_activity_part_of_rollup click TermObject href "../TermObject/" QueryIndex : model_activity_part_of_terms QueryIndex --> "*" TermObject : model_activity_part_of_terms click TermObject href "../TermObject/" QueryIndex : model_chemical_terms QueryIndex --> "*" TermObject : model_chemical_terms click TermObject href "../TermObject/" QueryIndex : model_taxon QueryIndex --> "*" TermObject : model_taxon click TermObject href "../TermObject/" QueryIndex : model_taxon_closure QueryIndex --> "*" TermObject : model_taxon_closure click TermObject href "../TermObject/" QueryIndex : model_taxon_rollup QueryIndex --> "*" TermObject : model_taxon_rollup 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_label
## Slots | Name | Cardinality and Range | Description | Inheritance | | --- | --- | --- | --- | | [taxon_label](taxon_label.md) | 0..1
[String](String.md) | The label of the primary taxon for the model | direct | | [number_of_activities](number_of_activities.md) | 0..1
[Integer](Integer.md) | The number of activities in a model | direct | | [number_of_enabled_by_terms](number_of_enabled_by_terms.md) | 0..1
[Integer](Integer.md) | The number of molecular entities or sets of entities in a model | direct | | [number_of_causal_associations](number_of_causal_associations.md) | 0..1
[Integer](Integer.md) | Total number of causal association edges connecting activities in a model | direct | | [length_of_longest_causal_association_path](length_of_longest_causal_association_path.md) | 0..1
[Integer](Integer.md) | The maximum number of hops along activities along the direction of causal flo... | direct | | [number_of_strongly_connected_components](number_of_strongly_connected_components.md) | 0..1
[Integer](Integer.md) | The number of distinct components that consist of activities that are connect... | direct | | [flattened_references](flattened_references.md) | *
[PublicationObject](PublicationObject.md) | All publication objects from the model across different levels combined in on... | direct | | [flattened_provided_by](flattened_provided_by.md) | *
[Object](Object.md) | All provided_by values from the model across different levels combined in one... | direct | | [flattened_contributors](flattened_contributors.md) | *
[String](String.md) | All contributor values from the model across different levels combined in one... | direct | | [flattened_evidence_terms](flattened_evidence_terms.md) | *
[EvidenceTermObject](EvidenceTermObject.md) | All evidence term objects from the model across different levels combined in ... | direct | | [model_activity_molecular_function_terms](model_activity_molecular_function_terms.md) | *
[TermObject](TermObject.md) | All MF terms for all activities | direct | | [model_activity_molecular_function_closure](model_activity_molecular_function_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of `model_activity_molecular_function_terms`... | direct | | [model_activity_molecular_function_rollup](model_activity_molecular_function_rollup.md) | *
[TermObject](TermObject.md) | The rollup of `model_activity_molecular_function_closure` to a GO subset or s... | direct | | [model_activity_occurs_in_terms](model_activity_occurs_in_terms.md) | *
[TermObject](TermObject.md) | All direct cellular component localization terms for all activities | direct | | [model_activity_occurs_in_closure](model_activity_occurs_in_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of `model_activity_occurs_in_terms`, over th... | direct | | [model_activity_occurs_in_rollup](model_activity_occurs_in_rollup.md) | *
[TermObject](TermObject.md) | The rollup of `model_activity_occurs_in_closure` to a GO subset or slim | direct | | [model_activity_enabled_by_terms](model_activity_enabled_by_terms.md) | *
[TermObject](TermObject.md) | All direct enabler terms for all activities | direct | | [model_activity_enabled_by_closure](model_activity_enabled_by_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of `model_activity_enabled_by_terms`, over t... | direct | | [model_activity_enabled_by_rollup](model_activity_enabled_by_rollup.md) | *
[TermObject](TermObject.md) | The rollup of `model_activity_enabled_by_closure` to a GO subset or slim | direct | | [model_activity_enabled_by_genes](model_activity_enabled_by_genes.md) | *
[TermObject](TermObject.md) | All direct enabler genes and genes that are part of enabler complexes for all... | direct | | [model_activity_part_of_terms](model_activity_part_of_terms.md) | *
[TermObject](TermObject.md) | All direct biological process terms for all activities | direct | | [model_activity_part_of_closure](model_activity_part_of_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of `model_activity_part_of_terms`, over the ... | direct | | [model_activity_part_of_rollup](model_activity_part_of_rollup.md) | *
[TermObject](TermObject.md) | The rollup of `model_activity_part_of_closure` to a GO subset or slim | direct | | [model_activity_has_input_terms](model_activity_has_input_terms.md) | *
[TermObject](TermObject.md) | All direct input terms for all activities | direct | | [model_activity_has_input_closure](model_activity_has_input_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of `model_activity_has_input_terms`, over th... | direct | | [model_activity_has_input_rollup](model_activity_has_input_rollup.md) | *
[TermObject](TermObject.md) | The rollup of `model_activity_has_input_closure` to a GO subset or slim | direct | | [model_chemical_terms](model_chemical_terms.md) | *
[TermObject](TermObject.md) | All molecule terms in the model that are chemical entities (e | direct | | [model_taxon](model_taxon.md) | *
[TermObject](TermObject.md) | The primary taxon term for the model, over the NCBITaxon:subClassOf relations... | direct | | [model_taxon_closure](model_taxon_closure.md) | *
[TermObject](TermObject.md) | The reflexive transitive closure of the taxon term for the model, over the NC... | direct | | [model_taxon_rollup](model_taxon_rollup.md) | *
[TermObject](TermObject.md) | The rollup of the taxon closure to a NCBITaxon subset or slim | direct | | [annoton_terms](annoton_terms.md) | *
[TermObject](TermObject.md) | | direct | | [start_activities](start_activities.md) | *
[Activity](Activity.md) | The set of activities that are the starting points of the model, i | direct | | [end_activities](end_activities.md) | *
[Activity](Activity.md) | The set of activities that are the end points of the model, i | direct | | [intermediate_activities](intermediate_activities.md) | *
[Activity](Activity.md) | The set of activities that are neither start nor end activities, i | direct | | [singleton_activities](singleton_activities.md) | *
[Activity](Activity.md) | The set of activities that have no causal associations, i | direct | | [number_of_start_activities](number_of_start_activities.md) | 0..1
[Integer](Integer.md) | The number of start activities in a model | direct | | [number_of_end_activities](number_of_end_activities.md) | 0..1
[Integer](Integer.md) | The number of end activities in a model | direct | | [number_of_intermediate_activities](number_of_intermediate_activities.md) | 0..1
[Integer](Integer.md) | The number of intermediate activities in a model | direct | | [number_of_singleton_activities](number_of_singleton_activities.md) | 0..1
[Integer](Integer.md) | The number of singleton activities in a model | direct | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [Model](Model.md) | [query_index](query_index.md) | range | [QueryIndex](QueryIndex.md) | ## 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:
  taxon_label:
    name: taxon_label
    description: The label of the primary taxon for the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: string
  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. This includes both explicit causal associations (e.g. "directly positively
      regulates") between activities and implicit causal associations between activities
      with shared input/output chemical entities.
    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_as_list: true
  flattened_provided_by:
    name: flattened_provided_by
    description: All provided_by values from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Object
    multivalued: true
    inlined_as_list: true
  flattened_contributors:
    name: flattened_contributors
    description: All contributor values from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: string
    multivalued: true
    inlined_as_list: true
  flattened_evidence_terms:
    name: flattened_evidence_terms
    description: All evidence term objects from the model across different levels
      combined in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: EvidenceTermObject
    multivalued: 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_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_as_list: true
  model_activity_molecular_function_rollup:
    name: model_activity_molecular_function_rollup
    description: The rollup of `model_activity_molecular_function_closure` to a GO
      subset or slim.
    comments:
    - added for completion but may not be useful in practice
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_occurs_in_terms:
    name: model_activity_occurs_in_terms
    description: All direct cellular component localization terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: 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]'
    description: The reflexive transitive closure of `model_activity_occurs_in_terms`,
      over the is_a and part_of relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_occurs_in_rollup:
    name: model_activity_occurs_in_rollup
    description: The rollup of `model_activity_occurs_in_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_enabled_by_terms:
    name: model_activity_enabled_by_terms
    description: All direct enabler terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_enabled_by_closure:
    name: model_activity_enabled_by_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    description: The reflexive transitive closure of `model_activity_enabled_by_terms`,
      over the is_a and part_of relationship types
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_enabled_by_rollup:
    name: model_activity_enabled_by_rollup
    description: The rollup of `model_activity_enabled_by_closure` to a GO subset
      or slim.
    comments:
    - added for completion but may not be useful in practice
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_enabled_by_genes:
    name: model_activity_enabled_by_genes
    description: All direct enabler genes and genes that are part of enabler complexes
      for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_part_of_terms:
    name: model_activity_part_of_terms
    description: All direct biological process terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: 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]'
    description: The reflexive transitive closure of `model_activity_part_of_terms`,
      over the is_a and part_of relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_part_of_rollup:
    name: model_activity_part_of_rollup
    description: The rollup of `model_activity_part_of_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_has_input_terms:
    name: model_activity_has_input_terms
    description: All direct input terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: 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]'
    description: The reflexive transitive closure of `model_activity_has_input_terms`,
      over the is_a relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_activity_has_input_rollup:
    name: model_activity_has_input_rollup
    description: The rollup of `model_activity_has_input_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_chemical_terms:
    name: model_chemical_terms
    description: All molecule terms in the model that are chemical entities (e.g.
      substrates or products) and not information biomacromolecules (e.g. gene products
      or complexes).
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_taxon:
    name: model_taxon
    description: The primary taxon term for the model, over the NCBITaxon:subClassOf
      relationship type. This is used to determine the primary taxon that the model
      is relevant to.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_taxon_closure:
    name: model_taxon_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    description: The reflexive transitive closure of the taxon term for the model,
      over the NCBITaxon:subClassOf relationship type. This is used to determine the
      set of taxa that are relevant to the model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined_as_list: true
  model_taxon_rollup:
    name: model_taxon_rollup
    description: The rollup of the taxon closure to a NCBITaxon subset or slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: 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_as_list: true
  start_activities:
    name: start_activities
    description: The set of activities that are the starting points of the model,
      i.e. those that have no incoming causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  end_activities:
    name: end_activities
    description: The set of activities that are the end points of the model, i.e.
      those that have no outgoing causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  intermediate_activities:
    name: intermediate_activities
    description: The set of activities that are neither start nor end activities,
      i.e. those that have both incoming and outgoing causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  singleton_activities:
    name: singleton_activities
    description: The set of activities that have no causal associations, i.e. those
      that are not connected to any other activity in the model.
    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:
  taxon_label:
    name: taxon_label
    description: The label of the primary taxon for the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: string
  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
    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
    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. This includes both explicit causal associations (e.g. "directly positively
      regulates") between activities and implicit causal associations between activities
      with shared input/output chemical entities.
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    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
    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
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: PublicationObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  flattened_provided_by:
    name: flattened_provided_by
    description: All provided_by values from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Object
    multivalued: true
    inlined: true
    inlined_as_list: true
  flattened_contributors:
    name: flattened_contributors
    description: All contributor values from the model across different levels combined
      in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
  flattened_evidence_terms:
    name: flattened_evidence_terms
    description: All evidence term objects from the model across different levels
      combined in one place
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: EvidenceTermObject
    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
    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
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_molecular_function_rollup:
    name: model_activity_molecular_function_rollup
    description: The rollup of `model_activity_molecular_function_closure` to a GO
      subset or slim.
    comments:
    - added for completion but may not be useful in practice
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    description: All direct cellular component localization terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    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]'
    description: The reflexive transitive closure of `model_activity_occurs_in_terms`,
      over the is_a and part_of relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_occurs_in_rollup:
    name: model_activity_occurs_in_rollup
    description: The rollup of `model_activity_occurs_in_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_enabled_by_terms:
    name: model_activity_enabled_by_terms
    description: All direct enabler terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_enabled_by_closure:
    name: model_activity_enabled_by_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf, BFO:0000050]'
    description: The reflexive transitive closure of `model_activity_enabled_by_terms`,
      over the is_a and part_of relationship types
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_enabled_by_rollup:
    name: model_activity_enabled_by_rollup
    description: The rollup of `model_activity_enabled_by_closure` to a GO subset
      or slim.
    comments:
    - added for completion but may not be useful in practice
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_enabled_by_genes:
    name: model_activity_enabled_by_genes
    description: All direct enabler genes and genes that are part of enabler complexes
      for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    description: All direct biological process terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    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]'
    description: The reflexive transitive closure of `model_activity_part_of_terms`,
      over the is_a and part_of relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_part_of_rollup:
    name: model_activity_part_of_rollup
    description: The rollup of `model_activity_part_of_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    description: All direct input terms for all activities
    from_schema: https://w3id.org/gocam
    rank: 1000
    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]'
    description: The reflexive transitive closure of `model_activity_has_input_terms`,
      over the is_a relationship type
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_activity_has_input_rollup:
    name: model_activity_has_input_rollup
    description: The rollup of `model_activity_has_input_closure` to a GO subset or
      slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_chemical_terms:
    name: model_chemical_terms
    description: All molecule terms in the model that are chemical entities (e.g.
      substrates or products) and not information biomacromolecules (e.g. gene products
      or complexes).
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_taxon:
    name: model_taxon
    description: The primary taxon term for the model, over the NCBITaxon:subClassOf
      relationship type. This is used to determine the primary taxon that the model
      is relevant to.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_taxon_closure:
    name: model_taxon_closure
    annotations:
      closure_computed_over:
        tag: closure_computed_over
        value: '[rdfs:subClassOf]'
    description: The reflexive transitive closure of the taxon term for the model,
      over the NCBITaxon:subClassOf relationship type. This is used to determine the
      set of taxa that are relevant to the model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_taxon_rollup:
    name: model_taxon_rollup
    description: The rollup of the taxon closure to a NCBITaxon subset or slim.
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: TermObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  start_activities:
    name: start_activities
    description: The set of activities that are the starting points of the model,
      i.e. those that have no incoming causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  end_activities:
    name: end_activities
    description: The set of activities that are the end points of the model, i.e.
      those that have no outgoing causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  intermediate_activities:
    name: intermediate_activities
    description: The set of activities that are neither start nor end activities,
      i.e. those that have both incoming and outgoing causal associations.
    from_schema: https://w3id.org/gocam
    rank: 1000
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: Activity
    multivalued: true
    inlined: false
  singleton_activities:
    name: singleton_activities
    description: The set of activities that have no causal associations, i.e. those
      that are not connected to any other activity in the model.
    from_schema: https://w3id.org/gocam
    rank: 1000
    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
    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
    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
    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
    owner: QueryIndex
    domain_of:
    - QueryIndex
    range: integer