reproschema.yaml

name: reproschema
id: http://schema.repronim.org/
version: 1.0.0
imports:
- linkml:types
prefixes:
  owl: http://www.w3.org/2002/07/owl#
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  xsd: http://www.w3.org/2001/XMLSchema#
  xml: http://www.w3.org/XML/1998/namespace
  nidm: http://purl.org/nidash/nidm#
  prov: http://www.w3.org/ns/prov#
  reproschema: http://schema.repronim.org/
  schema: http://schema.org/
  skos: http://www.w3.org/2004/02/skos/core#
  linkml: https://w3id.org/linkml/
default_range: string
slots:
  about:
    description: The subject matter of the Field.
    slot_uri: schema:about
  addProperties:
    title: addProperties
    description: An array of objects to describe the various properties added to assessments
      and Items.
    slot_uri: reproschema:addProperties
    multivalued: true
    range: AdditionalProperty
  additionalNotesObj:
    title: additional notes
    description:
      A set of objects to define notes in a field. For example, most Redcap and NDA
      data dictionaries have notes for each item which needs to be captured in reproschema.
    slot_uri: reproschema:additionalNotesObj
    multivalued: true
    any_of:
    - range: AdditionalNoteObj
  allow:
    title: allow
    description: An array of items indicating properties allowed on an activity or protocol.
    slot_uri: reproschema:allow
    multivalued: true
    range: AllowedType
  altLabel:
    title: alternate label
    description: The alternate label.
    slot_uri: skos:altLabel
    multivalued: true
    range: langString
    inlined: true
  associatedMedia:
    title: associatedMedia
    description: A media object that encodes this creative work. This property is a synonym for encoding.
    slot_uri: schema:associatedMedia
  audio:
    title: audio
    description: An audio object.
    slot_uri: schema:audio
    any_of:
    - range: uri
    - range: AudioObject
  category:
    description:
      Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the biolink entity type class.
      In an RDF database it should be a model class URI. This field is multi-valued.
    slot_uri: rdf:type
    range: uriorcurie
  choices:
    title: choices
    description: An array to list the available options for response of the Item.
    exact_mappings:
    - schema:itemListElement
    slot_uri: reproschema:choices
    multivalued: true
    any_of:
    - range: uri
    - range: Choice
  citation:
    slot_uri: schema:citation
    multivalued: true
    range: langString
    inlined: true
  column:
    title: column
    description: An element to define the column name where the note was taken from.
    slot_uri: reproschema:column
    range: string
  compute:
    title: computation
    description:
      An array of objects indicating computations in an activity or protocol and
      maps it to the corresponding Item. scoring logic is a subset of all computations
      that could be performed and not all computations will be scoring. For example,
      one may want to do conversion from one unit to another.
    slot_uri: reproschema:compute
    multivalued: true
    range: ComputeSpecification
    inlined: true
  contentUrl:
    slot_uri: schema:contentUrl
    range: uriorcurie
  cronTable:
    title: cronTable
    slot_uri: reproschema:cronTable
  datumType:
    title: datumType
    description: Indicates what type of datum the response is (e.g. range,count,scalar etc.) for the Item.
    slot_uri: reproschema:datumType
    any_of:
    - range: string
    - range: uri
  description:
    slot_uri: schema:description
    multivalued: true
    range: langString
    inlined: true
  endedAtTime:
    range: datetime
    slot_uri: prov:endedAtTime
  generated:
    slot_uri: prov:generated
    range: uri
  id:
    description:
      A unique identifier for an entity.
      Must be either a CURIE shorthand for a URI or a complete URI.
    slot_uri: schema:identifier
    range: uriorcurie
  image:
    title: image
    description:
      An image of the item. This can be a <a class="localLink" href="http://schema.org/URL">URL</a>
      or a fully described <a class="localLink" href="http://schema.org/ImageObject">ImageObject</a>.
    slot_uri: schema:image
    any_of:
      - range: ImageObject
      - range: uri
  inLanguage:
    slot_uri: schema:inLanguage
    range: string
  inputType:
    title: inputType
    description: An element to describe the input type of a Item.
    slot_uri: reproschema:inputType
  isAbout:
    title: isAbout
    description: A pointer to the node describing the item.
    slot_uri: reproschema:isAbout
    any_of:
    - range: uri
    - range: Activity
    - range: Item
    inlined: true
  isPartOf:
    slot_uri: schema:isPartOf
    range: Activity
  isProprietary:
    slot_uri: schema:isProprietary
    range: boolean
  isVis:
    title: visibility
    description:
      An element to describe (by boolean or conditional statement) visibility conditions of items in an assessment.
    slot_uri: reproschema:isVis
    any_of:
    - range: boolean
    - range: string
  jsExpression:
    title: JavaScript Expression
    description:
      A JavaScript expression for computations.
      A JavaScript expression to compute a score from other variables.
    slot_uri: reproschema:jsExpression
    range: string
  landingPage:
    title: Landing page content
    description: An element (by URL) to point to the protocol readme or landing page.
    slot_uri: reproschema:landingPage
    multivalued: true
    any_of:
    - range: uri
    - range: string
    - range: LandingPage
    inlined: true
  langstring_prefix:
    description:
      The language prefix component of a langString.
    key: true
    range: string
    required: true
  langstring_value:
    description:
      The value component of a langString.
    range: string
    required: true
  limit:
    title: limit
    description:
      An element to limit the duration (uses ISO 8601) this activity is allowed to
      be completed by once activity is available.
    slot_uri: reproschema:limit
    range: string
  maxRetakes:
    title: maxRetakes
    description: Defines number of times the item is allowed to be redone.
    slot_uri: reproschema:maxRetakes
    any_of:
    - range: integer
  maxValue:
    any_of:
    - range: float
    - range: integer
    slot_uri: schema:maxValue
  message:
    title: Message
    description: The message to be conditionally displayed for an item.
    slot_uri: reproschema:message
    multivalued: true
    range: langString
    inlined: true
  messages:
    title: messages
    description: An array of objects to define conditional messages in an activity or protocol.
    slot_uri: reproschema:messages
    multivalued: true
    range: MessageSpecification
  minValue:
    slot_uri: schema:minValue
    any_of:
    - range: float
    - range: integer
  multipleChoice:
    title: Multiple choice response expectation
    description: Indicates (by bool) if response for the Item has one or more answer.
    slot_uri: reproschema:multipleChoice
    range: boolean
  name:
    slot_uri: schema:name
    multivalued: true
    range: langString
    inlined: true
  order:
    title: Order
    description:
      An ordered list to describe the order in which the items of an assessment or
      protocol appear in the user interface.
    slot_uri: reproschema:order
    multivalued: true
    any_of:
    - range: uri
    - range: Activity
    - range: Item
  overrideProperties:
    title: overrideProperties
    description: An array of objects to override the various properties added to assessments and fields.
    slot_uri: reproschema:overrideProperties
    multivalued: true
    range: OverrideProperty
  preamble:
    title: Preamble
    description: The preamble for an assessment.
    slot_uri: reproschema:preamble
    multivalued: true
    range: langString
    inlined: true
  prefLabel:
    title: preferred label
    description: The preferred label.
    slot_uri: skos:prefLabel
    multivalued: true
    range: langString
    inlined: true
  question:
    slot_uri: schema:question
    multivalued: true
    range: langString
    inlined: true
  randomMaxDelay:
    title: randomMaxDelay
    description:
      Present activity/item within some random offset of activity available time up
      to the maximum specified by this ISO 8601 duration
    slot_uri: reproschema:randomMaxDelay
    range: string
  readonlyValue:
    slot_uri: schema:readonlyValue
    range: boolean
  responseOptions:
    title: Response options
    description: An element (object or by URL)to describe the properties of response of the Item.
    slot_uri: reproschema:responseOptions
    any_of:
    - range: uri
    - range: ResponseOption
  schedule:
    title: Schedule
    description: An element to set make activity available/repeat info using ISO 8601 repeating interval format.
    slot_uri: reproschema:schedule
    range: string
  schemaVersion:
    slot_uri: schema:schemaVersion
    range: string
  shuffle:
    title: Shuffle
    description: An element (bool) to determine if the list of items is shuffled or in order.
    slot_uri: reproschema:shuffle
    range: boolean
  source:
    title: source
    description: An element to define the source (eg. RedCap, NDA) where the note was taken from.
    slot_uri: reproschema:source
    range: string
  statusOptions:
    title: Status options
    description:
      Provides information on whether or not an Item wants to be accompanied
      by the additional status option(s) defined in "statusOptions"
    slot_uri: reproschema:statusOptions
  startedAtTime:
    range: datetime
    slot_uri: prov:startedAtTime
  subject_id:
    slot_uri: nidm:subject_id
    range: string
  ui:
    title: UI
    description:
      An element to control UI specifications. Originally @nest in jsonld, but using a class in the model.
    slot_uri: reproschema:ui
    range: UI
  unitOptions:
    title: unitOptions
    description:
      A list of objects to represent a human displayable name alongside the more formal
      value for units.
    slot_uri: reproschema:unitOptions
    multivalued: true
    range: UnitOption
  url:
    slot_uri: schema:url
    range: uri
  used:
    slot_uri: prov:used
    multivalued: true
  value:
    title: value
    description: The value for each option in choices or in additionalNotesObj
    slot_uri: schema:value
    any_of:
    - range: float
    - range: integer
    - range: boolean
    - range: StructuredValue
    - range: langString
    - range: uri
    - range: string
    - range: MissingType
    inlined: true
  valueType:
    title: The type of the response
    description: The type of the response of an item. For example, string, integer, etc.
    slot_uri: reproschema:valueType
    multivalued: true
    range: string
  valueRequired:
    slot_uri: schema:valueRequired
    range: boolean
  variableName:
    title: variableName
    description: The name used to represent an item.
    slot_uri: reproschema:variableName
    range: langString
  version:
    slot_uri: schema:version
    range: string
  video:
    slot_uri: schema:video
    any_of:
    - range: VideoObject
    - range: uri
  wasAssociatedWith:
    slot_uri: prov:wasAssociatedWith
    range: SoftwareAgent
  wasAttributedTo:
    slot_uri: prov:wasAttributedTo
    range: Participant
classes:
  Activity:
    title: Activity
    description: An assessment in a protocol.
    is_a: Thing
    slots:
    - about
    - altLabel
    - associatedMedia
    - citation
    - compute
    - cronTable
    - description
    - image
    - isProprietary
    - messages
    - preamble
    - prefLabel
    - schemaVersion
    - ui
    - version
    class_uri: reproschema:Activity
  AdditionalNoteObj:
    title: Additional Notes Object
    description:
      A set of objects to define notes in a Item. For example, most Redcap and NDA
      data dictionaries have notes for each item which needs to be captured in reproschema
    is_a: Thing
    slots:
    - column
    - source
    - value
    class_uri: reproschema:AdditionalNoteObj
  AdditionalProperty:
    title: Additional properties
    description: An object to describe the various properties added to assessments and Items.
    is_a: Thing
    slots:
    - allow
    - isAbout
    - isVis
    - limit
    - maxRetakes
    - prefLabel
    - randomMaxDelay
    - schedule
    - valueRequired
    - variableName
    - ui
    class_uri: reproschema:AdditionalProperty
  AudioObject:
    is_a: MediaObject
    class_uri: schema:AudioObject
  Agent:
    class_uri: prov:Agent
  Choice:
    title: Response choice
    description: An object to describe a response option.
    is_a: Thing
    slots:
    - name
    - image
    - value
    class_uri: reproschema:Choice
  ComputeSpecification:
    title: Compute Specification
    description: An object to define computations in an activity or protocol.
    is_a: Thing
    slots:
    - jsExpression
    - variableName
    class_uri: reproschema:ComputeSpecification
  ImageObject:
    is_a: MediaObject
    class_uri: schema:ImageObject
  Item:
    title: Item in an activity
    description: An item in an assessment.
    is_a: Thing
    slots:
    - about
    - additionalNotesObj
    - altLabel
    - associatedMedia
    - audio
    - description
    - image
    - isPartOf
    - preamble
    - prefLabel
    - question
    - responseOptions
    - schemaVersion
    - ui
    - version
    - video
    class_uri: reproschema:Field
  LandingPage:
    title: Landing Page
    description: An object to define the landing page of a protocol.
    is_a: Thing
    slots:
    - inLanguage
    class_uri: reproschema:LandingPage
  langString:
    description: RDF langString tuple
    slots:
    - langstring_prefix
    - langstring_value
    class_uri: rdf:langString
  MediaObject:
    title: Media Object
    description: A media object, such as an image, video, audio, or text object embedded in a web page or a downloadable dataset.
    is_a: Thing
    class_uri: schema:MediaObject
    slots:
      - inLanguage
      - contentUrl
    slot_usage:
      contentUrl:
        required: true
  MessageSpecification:
    title: Message Specification
    description: An object to define messages in an activity or protocol.
    is_a: Thing
    slots:
    - jsExpression
    - message
    class_uri: reproschema:MessageSpecification
  OverrideProperty:
    title: Additional properties
    description: An object to override the various properties added to assessments and Items.
    is_a: Thing
    slots:
    - isAbout
    - isVis
    - limit
    - maxRetakes
    - prefLabel
    - randomMaxDelay
    - schedule
    - valueRequired
    - variableName
    class_uri: reproschema:OverrideProperty
  Participant:
    title: Participant
    description: An Agent describing characteristics associated with a participant.
    is_a: Agent
    slots:
      - id
      - subject_id
    class_uri: reproschema:Participant
  Protocol:
    title: Protocol
    description: A representation of a study which comprises one or more assessments.
    is_a: Thing
    slots:
    - about
    - altLabel
    - associatedMedia
    - compute
    - cronTable
    - description
    - landingPage
    - messages
    - preamble
    - prefLabel
    - schemaVersion
    - ui
    - version
    class_uri: reproschema:Protocol
  Response: # multiple types
    title: Response
    description: Describes the response of an item.
    is_a: Thing
    slots:
    - isAbout
    - value
    - wasAttributedTo
    class_uri: reproschema:Response
  ResponseActivity: # multiple types
    title: ResponseActivity
    description:
      Captures information about some action that took place. It also links to information
      (entities) that were used during the activity
    is_a: Thing
    slots:
      - endedAtTime
      - generated
      - inLanguage
      - startedAtTime
      - used
      - wasAssociatedWith
    class_uri: reproschema:ResponseActivity
  ResponseOption:
    title: Response option
    description: An element (object or by URL)to describe the properties of response of the Item.
    is_a: Thing
    slots:
    - choices
    - datumType
    - maxValue
    - minValue
    - multipleChoice
    - unitOptions
    - valueType
    class_uri: reproschema:ResponseOption
  SoftwareAgent:
    title: Software Agent
    description:
      Captures information about some action that took place. It also links to information
      (entities) that were used during the activity
    is_a: Thing
    slots:
    - version
    - url
    class_uri: reproschema:SoftwareAgent
  StructuredValue:
    is_a: Thing
    class_uri: schema:StructuredValue
  Thing:
    slots:
      - id
      - name
      - category
    class_uri: schema:Thing
  UI:
    title: UI properties
    description: A group of properties related to UI.
    slots:
      - order
      - addProperties
      - overrideProperties
      - shuffle
      - allow
      - inputType
      - readonlyValue
    class_uri: reproschema:UI
  UnitOption:
    title: Unit options
    description: An object to represent a human displayable name alongside the more formal value for units.
    is_a: Thing
    slots:
    - prefLabel
    - value
    slot_usage:
      value:
        any_of:
          - range: uri
          - range: langString
    class_uri: reproschema:UnitOption
  VideoObject:
    title: Video Object
    is_a: MediaObject
    class_uri: schema:VideoObject

enums:
  AllowedType:
    permissible_values:
      reproschema:AllowAltResponse:
        title: AllowAltResponse
        description: Indicates (by boolean) if alternate responses are allowed or not.
        meaning: reproschema:AllowAltResponse
      reproschema:AllowExport:
        title: AllowExport
        description: Indicates (by boolean) if data can be exported or not.
        meaning: reproschema:AllowExport
      reproschema:AllowReplay:
        title: AllowReplay
        description: Indicates (by boolean) if items can be replayed or not.
        meaning: reproschema:AllowReplay
      reproschema:AllowSkip:
        title: AllowSkip
        description: Indicates (by boolean) if items can be skipped or not.
        meaning: reproschema:AllowSkip
      reproschema:AutoAdvance:
        title: AutoAdvance
        description: Indicates (by boolean) if assessments in a protocol can auto advance or not.
        meaning: reproschema:AutoAdvance
      reproschema:DisableBack:
        title: DisableBack
        description: Indicates (by boolean) if we can go back to a completed assessment in a protocol.
        meaning: reproschema:DisableBack
  MissingType:
    permissible_values:
      reproschema:Skipped:
        title: Skipped
        description: An element to describe the choice when the item is skipped.
        meaning: reproschema:Skipped
      reproschema:DontKnow:
        title: DontKnow
        description: An element to describe the choice when response is not known.
        meaning: reproschema:DontKnow
      reproschema:Unknown:
        title: Unknown
        description: An element to describe the choice when the reason for missing response is unknown.
        meaning: reproschema:Unknown
      reproschema:TimedOut:
        title: TimedOut
        description: A boolean element to describe if the response did not occur within the prescribed time.
        meaning: reproschema:TimedOut