Class: Activity (Activity)

An action or set of actions performed by an agent, that occurs over a period of time. Activities may use, generate, modify, move, or destroy one or more entities.

Comments

Activities relevant to scientific knowledge generation, and include things like observations of the natural world, designing and performing experiments, data analysis and transformation, publishing research results, data curation and interpretation, and assessment and care of patients in clinical settings. These activities may produce information that gets encoded in sharable artifacts which are used to generate scientific knowledge. Agents can play different types of roles in the generation and use of such artifacts.

URI: sepio_linkml:Activity

classDiagram class Activity click Activity href "../Activity" Entity <|-- Activity click Entity href "../Entity" Activity <|-- Contribution click Contribution href "../Contribution" Activity : alternativeLabels Activity : date Activity : description Activity : extensions Activity --> "*" Extension : extensions click Extension href "../Extension" Activity : id Activity : identifiers Activity : input Activity --> "*" Entity : input click Entity href "../Entity" Activity : label Activity : output Activity --> "*" Entity : output click Entity href "../Entity" Activity : performedBy Activity --> "*" Agent : performedBy click Agent href "../Agent" Activity : specifiedBy Activity --> "*" Method : specifiedBy click Method href "../Method" Activity : subtype Activity --> "0..1" Coding : subtype click Coding href "../Coding" Activity : type

Inheritance

Entity
- Activity
  - Contribution

Slots

Direct slots

subtype --> Coding [0..1]

A specific type of activity the Activity instance represents.

Implementation Guidance

* This attribute can be used to report a specific type for the Activity, in cases where a model does not define Activity subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application.

date --> date [0..1]

The date that the Activity was completed.

Implementation Guidance

* By convention, populate this attribute with the date the activity was completed (e.g. in cases where the activity spans multiple days). The date SHOULD be formatted as a date string in ISO format "YYYY-MM-DD".

performedBy --> Agent [*]

An Agent who participated in executing the Activity.

specifiedBy --> Method [*]

A method that was followed in performing an Activity, that describes how it was executed.

input --> Entity [*]

An entity that was input into the Activity (could be material or information)

output --> Entity [*]

An entity that was output from the Activity (could be material or information)

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.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Activity
description: An action or set of actions performed by an agent, that occurs over a
  period of time. Activities may use, generate, modify, move, or destroy one or more
  entities.
title: Activity
comments:
- Activities relevant to scientific knowledge generation, and include things like
  observations of the natural world, designing and performing experiments, data analysis
  and transformation, publishing research results, data curation and interpretation,
  and assessment and care of patients in clinical settings.  These activities may
  produce information that gets encoded in sharable artifacts which are used to generate
  scientific knowledge. Agents can play different types of roles in the generation
  and use of such artifacts.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: Entity
attributes:
  subtype:
    name: subtype
    description: A specific type of activity the Activity instance represents.
    comments:
    - This attribute can be used to report a specific type for the Activity, in cases
      where a model does not define Activity subclasses for this purpose.  Implementers
      can define their own set of data set type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  date:
    name: date
    description: The date that the Activity was completed.
    comments:
    - By convention, populate this attribute with the date the activity was completed
      (e.g.  in cases where the activity spans multiple days). The date SHOULD be
      formatted as a date string in ISO format "YYYY-MM-DD".
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - Activity
    range: date
    required: false
    multivalued: false
  performedBy:
    name: performedBy
    description: An Agent who participated in executing the Activity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - Activity
    range: Agent
    required: false
    multivalued: true
  specifiedBy:
    name: specifiedBy
    description: A method that was followed in performing an Activity, that describes
      how it was executed.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - InformationEntity
    - Activity
    range: Method
    required: false
    multivalued: true
  input:
    name: input
    description: An entity that was input into the Activity (could be material or
      information)
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - Activity
    range: Entity
    required: false
    multivalued: true
  output:
    name: output
    description: An entity that was output from the Activity (could be material or
      information)
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - Activity
    range: Entity
    required: false
    multivalued: true

Induced

name: Activity
description: An action or set of actions performed by an agent, that occurs over a
  period of time. Activities may use, generate, modify, move, or destroy one or more
  entities.
title: Activity
comments:
- Activities relevant to scientific knowledge generation, and include things like
  observations of the natural world, designing and performing experiments, data analysis
  and transformation, publishing research results, data curation and interpretation,
  and assessment and care of patients in clinical settings.  These activities may
  produce information that gets encoded in sharable artifacts which are used to generate
  scientific knowledge. Agents can play different types of roles in the generation
  and use of such artifacts.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: Entity
attributes:
  subtype:
    name: subtype
    description: A specific type of activity the Activity instance represents.
    comments:
    - This attribute can be used to report a specific type for the Activity, in cases
      where a model does not define Activity subclasses for this purpose.  Implementers
      can define their own set of data set type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: subtype
    owner: Activity
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  date:
    name: date
    description: The date that the Activity was completed.
    comments:
    - By convention, populate this attribute with the date the activity was completed
      (e.g.  in cases where the activity spans multiple days). The date SHOULD be
      formatted as a date string in ISO format "YYYY-MM-DD".
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: date
    owner: Activity
    domain_of:
    - Activity
    range: date
    required: false
    multivalued: false
  performedBy:
    name: performedBy
    description: An Agent who participated in executing the Activity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: performedBy
    owner: Activity
    domain_of:
    - Activity
    range: Agent
    required: false
    multivalued: true
  specifiedBy:
    name: specifiedBy
    description: A method that was followed in performing an Activity, that describes
      how it was executed.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: specifiedBy
    owner: Activity
    domain_of:
    - InformationEntity
    - Activity
    range: Method
    required: false
    multivalued: true
  input:
    name: input
    description: An entity that was input into the Activity (could be material or
      information)
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: input
    owner: Activity
    domain_of:
    - Activity
    range: Entity
    required: false
    multivalued: true
  output:
    name: output
    description: An entity that was output from the Activity (could be material or
      information)
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: output
    owner: Activity
    domain_of:
    - Activity
    range: Entity
    required: false
    multivalued: true
  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: Activity
    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: Activity
    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: Activity
    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: Activity
    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: Activity
    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: Activity
    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: Activity
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true