Class: Agent (Agent)

An autonomous actor (person, organization, or software agent) that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.

Comments

Agents perform activities and make contributions to entities. An agent can be an individual person, an organization of multiple individuals acting together, or a computational agent such as a software program or automated pipeline.
Agents can belong to organizations, and act on behalf or in the context of an organizational affiliation when contributing to an entity. For example, curators generating these variant pathogenicity interpretations may do so in the context of their work with the ClinGen organization, which provides administrative, technical, and funding support for their contributions.

URI: sepio_linkml:Agent

classDiagram class Agent click Agent href "../Agent" Entity <|-- Agent click Entity href "../Entity" Agent : alternativeLabels Agent : description Agent : extensions Agent --> "*" Extension : extensions click Extension href "../Extension" Agent : id Agent : identifiers Agent : label Agent : name Agent : subtype Agent : type

Inheritance

Entity
- Agent

Slots

Direct slots

subtype --> String [0..1]

A specific type of agent the Agent object represents. Must be one of {person, organization, software}

Implementation Guidance

* At present, there are no subclasses in the model representing the three high level types of Agent (person, organization, or software). If it is determined that there are enough unique properties that need to be defined for these subtypes, separate classes may be defined in a future release.

name --> String [0..1]

The given name of the Agent.

Inherited slots

id --> String [1]

The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference one object from another.

Inherited from: Entity

Implementation Guidance

* Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to reuse an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context.

identifiers --> String [*]

A globally-unique 'business' identifier or accession number for the real-world entity represented by a data object. These are typically assigned by an external system or authority, and used to connect entities and share content across different systems.

Inherited from: Entity

Implementation Guidance

* Preferred values for this attribute are CURIEs or URIs - so the system that provisioned the identifier is clear.
* A given real world entity - e.g. a genetic variant - may have many business identifiers defined by different systems, which can be captured in the "identifiers" property to indicate that they represent the same thing.

type --> String [1]

The name of the class that is instantiated by a data object representing the Entity.

Inherited from: Entity

Implementation Guidance

* MUST be the label of a concrete class from the data model.

label --> String [0..1]

A primary name for the Entity.

Inherited from: Entity

alternativeLabels --> String [*]

Alternative name(s) for the Entity.

Inherited from: Entity

description --> String [0..1]

A free text description of the Entity.

Inherited from: Entity

extensions --> Extension [*]

A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.

Inherited from: Entity

Implementation Guidance

* Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.

Usages

used by	used in	type	used
Activity	performedBy	range	Agent
Contribution	contributor	range	Agent
Contribution	performedBy	range	Agent

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/sepio-framework/sepio-linkml

Mappings

Mapping Type	Mapped Value
self	sepio_linkml:Agent
native	sepio_linkml:Agent

LinkML Source

Direct

name: Agent
description: An autonomous actor (person, organization, or software agent) that bears
  some form of responsibility for an activity taking place,  for the existence of
  an entity, or for another agent's activity.
title: Agent
comments:
- Agents perform activities and make contributions to entities. An agent can be an
  individual person, an organization of multiple individuals acting together, or a
  computational agent such as a software program or automated pipeline.
- Agents can belong to organizations, and act on behalf or in the context of an organizational
  affiliation when contributing to an entity. For example, curators generating these
  variant pathogenicity interpretations may do so in the context of their work with
  the ClinGen organization, which provides administrative, technical, and funding
  support for their contributions.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: Entity
attributes:
  subtype:
    name: subtype
    description: A specific type of agent the Agent object represents. Must be one
      of {person, organization, software}
    comments:
    - At present, there are no subclasses in the model representing the three high
      level types of Agent (person, organization, or software). If it is determined
      that there are enough unique properties that need to be defined for these subtypes,
      separate classes may be defined in a future release.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  name:
    name: name
    description: The given name of the Agent.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - Agent
    - Qualifier
    - Extension
    - Characteristic
    range: string
    required: false
    multivalued: false

Induced

name: Agent
description: An autonomous actor (person, organization, or software agent) that bears
  some form of responsibility for an activity taking place,  for the existence of
  an entity, or for another agent's activity.
title: Agent
comments:
- Agents perform activities and make contributions to entities. An agent can be an
  individual person, an organization of multiple individuals acting together, or a
  computational agent such as a software program or automated pipeline.
- Agents can belong to organizations, and act on behalf or in the context of an organizational
  affiliation when contributing to an entity. For example, curators generating these
  variant pathogenicity interpretations may do so in the context of their work with
  the ClinGen organization, which provides administrative, technical, and funding
  support for their contributions.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: Entity
attributes:
  subtype:
    name: subtype
    description: A specific type of agent the Agent object represents. Must be one
      of {person, organization, software}
    comments:
    - At present, there are no subclasses in the model representing the three high
      level types of Agent (person, organization, or software). If it is determined
      that there are enough unique properties that need to be defined for these subtypes,
      separate classes may be defined in a future release.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    alias: subtype
    owner: Agent
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  name:
    name: name
    description: The given name of the Agent.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: name
    owner: Agent
    domain_of:
    - Agent
    - Qualifier
    - Extension
    - Characteristic
    range: string
    required: false
    multivalued: false
  id:
    name: id
    description: The 'logical' identifier of the entity in the system of record, e.g.
      a UUID.  This 'id' is unique within a given system, but may or may not be globally
      unique outside the system. It is used within a system to reference one object
      from another.
    comments:
    - Note that it is common for implementers to create their own internal logical
      ids - typically a serially or randomly generated value like a UUID that is assigned
      to the data object as it is created in a system. But an implementer may choose
      to reuse an existing, globally unique id from an external system or authority
      for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique
      within the implementing system, and can be used to reference the identified
      object in this context.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: id
    owner: Agent
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  identifiers:
    name: identifiers
    description: A globally-unique 'business' identifier or accession number for the
      real-world entity represented by a data object. These are typically assigned
      by an external system or authority, and used to connect entities and share content
      across different systems.
    comments:
    - Preferred values for this attribute are CURIEs or URIs - so the system that
      provisioned the identifier is clear.
    - A given real world entity - e.g. a genetic variant - may have many business
      identifiers defined by different systems, which can be captured in the "identifiers"
      property to indicate that they represent the same thing.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: identifiers
    owner: Agent
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  type:
    name: type
    description: The name of the class that is instantiated by a data object representing
      the Entity.
    comments:
    - MUST be the label of a concrete class from the data model.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: type
    owner: Agent
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: label
    owner: Agent
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
    multivalued: false
  alternativeLabels:
    name: alternativeLabels
    description: Alternative name(s) for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: alternativeLabels
    owner: Agent
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  description:
    name: description
    description: A free text description of the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: description
    owner: Agent
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: false
  extensions:
    name: extensions
    description: A list of extensions to the Entity, that allow for capture of information
      not directly supported by elements defined in the model.
    comments:
    - Extension objects have a key-value data structure that allows definition of
      custom fields in the data itself. Extensions are not expected to be natively
      understood, but may be used for pre-negotiated exchange of message attributes
      between systems.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: extensions
    owner: Agent
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true