Class: Model

A model of a biological program consisting of a set of causally connected activities.

classDiagram class Model click Model href "../Model" Model : activities Model --> "*" Activity : activities click Activity href "../Activity" Model : additional_taxa Model --> "*" TaxonTermObject : additional_taxa click TaxonTermObject href "../TaxonTermObject" Model : comments Model : id Model : objects Model --> "*" Object : objects click Object href "../Object" Model : provenances Model --> "*" ProvenanceInfo : provenances click ProvenanceInfo href "../ProvenanceInfo" Model : query_index Model --> "0..1" QueryIndex : query_index click QueryIndex href "../QueryIndex" Model : status Model --> "0..1" ModelStateEnum : status click ModelStateEnum href "../ModelStateEnum" Model : taxon Model --> "0..1" TaxonTermObject : taxon click TaxonTermObject href "../TaxonTermObject" Model : title

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 Uriorcurie	The identifier of the model	direct
title	1 String	The human-readable descriptive title of the model	direct
taxon	0..1 TaxonTermObject	The primary taxon that the model is about	direct
additional_taxa	* TaxonTermObject	Additional taxa that the model is about	direct
status	0..1 ModelStateEnum	The status of the model in terms of its progression along the developmental l...	direct
comments	* String	Curator-provided comments about the model	direct
activities	* Activity	All of the activities that are part of the model	direct
objects	* Object	All of the objects that are part of the model	direct
provenances	* ProvenanceInfo	Model-level provenance information	direct
query_index	0..1 QueryIndex	An optional object that contains the results of indexing a model with various...	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Model
description: A model of a biological program consisting of a set of causally connected
  activities.
from_schema: https://w3id.org/gocam
attributes:
  id:
    name: id
    description: The identifier of the model. Should be in gocam namespace.
    from_schema: https://w3id.org/gocam
    rank: 1000
    identifier: true
    domain_of:
    - Model
    - Activity
    - Object
    range: uriorcurie
    required: true
  title:
    name: title
    description: The human-readable descriptive title of the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    slot_uri: dct:title
    domain_of:
    - Model
    required: true
  taxon:
    name: taxon
    description: The primary taxon that the model is about
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    range: TaxonTermObject
  additional_taxa:
    name: additional_taxa
    description: Additional taxa that the model is about
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    range: TaxonTermObject
    multivalued: true
  status:
    name: status
    description: The status of the model in terms of its progression along the developmental
      lifecycle
    from_schema: https://w3id.org/gocam
    aliases:
    - model state
    rank: 1000
    slot_uri: pav:status
    domain_of:
    - Model
    range: ModelStateEnum
  comments:
    name: comments
    description: Curator-provided comments about the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    slot_uri: rdfs:comment
    domain_of:
    - Model
    multivalued: true
  activities:
    name: activities
    description: All of the activities that are part of the model
    comments:
    - this slot is conditionally required. It is optional for models in development
      state (because a curator may need to instantiate a Model before populating it
      with activities), but is required for production models. See the associated
      rule.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    range: Activity
    multivalued: true
    inlined: true
    inlined_as_list: true
  objects:
    name: objects
    description: All of the objects that are part of the model. This includes terms
      as well as publications and database objects like gene. This is not strictly
      part of the data managed by the model, it is for convenience, and should be
      refreshed from outside.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    range: Object
    multivalued: true
    inlined: true
    inlined_as_list: true
  provenances:
    name: provenances
    description: Model-level provenance information
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    - Activity
    - EvidenceItem
    - Association
    range: ProvenanceInfo
    multivalued: true
    inlined: true
    inlined_as_list: true
  query_index:
    name: query_index
    description: An optional object that contains the results of indexing a model
      with various summary statistics and retrieval indices.
    comments:
    - This is typically not populated in the primary transactional store (OLTP processing),
      because the values will be redundant with the primary edited components of the
      model. It is intended to be populated in batch *after* editing, and then used
      for generating reports, or for indexing in web applications.
    from_schema: https://w3id.org/gocam
    rank: 1000
    domain_of:
    - Model
    range: QueryIndex
rules:
- preconditions:
    slot_conditions:
      state:
        name: state
        equals_string: production
  postconditions:
    slot_conditions:
      activities:
        name: activities
        required: true
  title: Production rules must have at least one activity

Induced

name: Model
description: A model of a biological program consisting of a set of causally connected
  activities.
from_schema: https://w3id.org/gocam
attributes:
  id:
    name: id
    description: The identifier of the model. Should be in gocam namespace.
    from_schema: https://w3id.org/gocam
    rank: 1000
    identifier: true
    alias: id
    owner: Model
    domain_of:
    - Model
    - Activity
    - Object
    range: uriorcurie
  title:
    name: title
    description: The human-readable descriptive title of the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    slot_uri: dct:title
    alias: title
    owner: Model
    domain_of:
    - Model
    range: string
    required: true
  taxon:
    name: taxon
    description: The primary taxon that the model is about
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: taxon
    owner: Model
    domain_of:
    - Model
    range: TaxonTermObject
  additional_taxa:
    name: additional_taxa
    description: Additional taxa that the model is about
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: additional_taxa
    owner: Model
    domain_of:
    - Model
    range: TaxonTermObject
    multivalued: true
  status:
    name: status
    description: The status of the model in terms of its progression along the developmental
      lifecycle
    from_schema: https://w3id.org/gocam
    aliases:
    - model state
    rank: 1000
    slot_uri: pav:status
    alias: status
    owner: Model
    domain_of:
    - Model
    range: ModelStateEnum
  comments:
    name: comments
    description: Curator-provided comments about the model
    from_schema: https://w3id.org/gocam
    rank: 1000
    slot_uri: rdfs:comment
    alias: comments
    owner: Model
    domain_of:
    - Model
    range: string
    multivalued: true
  activities:
    name: activities
    description: All of the activities that are part of the model
    comments:
    - this slot is conditionally required. It is optional for models in development
      state (because a curator may need to instantiate a Model before populating it
      with activities), but is required for production models. See the associated
      rule.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: activities
    owner: Model
    domain_of:
    - Model
    range: Activity
    multivalued: true
    inlined_as_list: true
  objects:
    name: objects
    description: All of the objects that are part of the model. This includes terms
      as well as publications and database objects like gene. This is not strictly
      part of the data managed by the model, it is for convenience, and should be
      refreshed from outside.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: objects
    owner: Model
    domain_of:
    - Model
    range: Object
    multivalued: true
    inlined_as_list: true
  provenances:
    name: provenances
    description: Model-level provenance information
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: provenances
    owner: Model
    domain_of:
    - Model
    - Activity
    - EvidenceItem
    - Association
    range: ProvenanceInfo
    multivalued: true
    inlined_as_list: true
  query_index:
    name: query_index
    description: An optional object that contains the results of indexing a model
      with various summary statistics and retrieval indices.
    comments:
    - This is typically not populated in the primary transactional store (OLTP processing),
      because the values will be redundant with the primary edited components of the
      model. It is intended to be populated in batch *after* editing, and then used
      for generating reports, or for indexing in web applications.
    from_schema: https://w3id.org/gocam
    rank: 1000
    alias: query_index
    owner: Model
    domain_of:
    - Model
    range: QueryIndex
rules:
- preconditions:
    slot_conditions:
      state:
        name: state
        equals_string: production
  postconditions:
    slot_conditions:
      activities:
        name: activities
        required: true
  title: Production rules must have at least one activity