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The schema

Overview

A simplistic way to describe the Reprochema is to say it is organized in a hierarchical manner with roughly 3 levels with a schema describing each level.

  1. The highest level is the protocol level that originally define a set of assessments or questionnaires to be included in a given study. This schema is defined by the Protocol schema.

  2. The second level is the activity level that describe a given questionnaire. This level would describe all the questions of this assessment: for example all the items of the Edinburgh handedness inventory would constitute one activity. This schema is defined by the Activity schema.

  3. At a lower level we have the item level where each item represents a question from a given assessment. On top of containing the text of the actual question, the schema at this level can contain additional information such as the expected format of the item for the user interface: a boolean (if this is a yes/no question), a multiple choice (with a list of the response choices), a float or an integer (if a numerical value is expected)... This schema is defined by the Field schema.

reproschema

You can see an example of those in the examples folder

There are in fact more levels than this each and each level has its own schema:

  • all of the schemas can be found in the terms folder
  • the Reproschema actually allows for a more complex level nesting than the one described above (e.g you can have an activity within an activity)
  • all the properties of each level are described below in the Properties of ReproSchema objects section

Detailed description

The core model of ReproSchema was initially derived from the CEDAR Metadata Model. To accommodate the needs of neuroimaging and other clinical and behavioral protocols and assessments the schema has evolved significantly. These changes include:

  1. Alignment with schema.org and NIDM. We have used schema.org classes and properties where it maps on to the needs of the model and extended the model with NIDM elements to harmonize across ReproNim projects.

  2. Allowing for structured nested elements in a schema Protocol > Activity > [Activity | Field > ResponseOption]. This nested structure provides a flexible schema to represent nested activities, which are common in biomedical and other domains.

Protocol
├── Activity
│   ├── Field
│   │   └── ResponseOption
│   └── Field
│   │   └── ResponseOption
│   ├── Activity
│   │   ├── Field
│   │   │   └── ResponseOption
│   │   ...
│   ...
├── Activity
│   ...
...

  1. Interaction with Git/Github or another Web service to deliver a new protocol, ativity or field with a persistent URI, while tracking changes associated with any of these elements. By making every field represented through a persistent URI, a data collection instrument can link the responses to the exact field that was used.

  2. Addition of computable elements that are derived from the values entered by a participant.

  3. Allowing for user interface (UI) elements that allow interaction between the schema and any implementation that allows collecting data using the schema. By providing some additional UI elements the provider can guide an implementer to allow for more complex data collection behavior.

The ReproSchema-UI is a prototype implementation of an UI that leverages these different elements of the schema.

Properties of ReproSchema objects

This section lists the core ReproSchema objects and their allowed properties.

Protocol

A representation of a study which comprises one or more assessments.

URI: http://schema.repronim.org/Protocol

Name Description URI
addProperties An array of objects to describe the various properties added to assessments and fields. http://schema.repronim.org/addProperties
allow An array of items indicating properties allowed on an activity or protocol http://schema.repronim.org/allow
compute An array of objects indicating computations in an activity or protocol and maps it to the corresponding Field 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. http://schema.repronim.org/compute
landingPage An element (by URL) to point to the protocol readme or landing page. http://schema.repronim.org/landingPage
messages An array of objects to define conditional messages in an activity or protocol. http://schema.repronim.org/messages
order An ordered list to describe the order in which the items of an assessment or protocol appear in the user interface. http://schema.repronim.org/order
overrideProperties An array of objects to override the various properties added to assessments and fields. http://schema.repronim.org/overrideProperties
preamble The preamble for an assessment http://schema.repronim.org/preamble
shuffle An element (bool) to determine if the list of items is shuffled or in order. http://schema.repronim.org/shuffle
about The subject matter of the Field. http://schema.org/about
audio An embedded audio object. http://schema.org/audio
description A description of the item. http://schema.org/description
image An image of the item. This can be a URL or a fully described ImageObject. http://schema.org/image
schemaVersion Indicates (by URL or string) a particular version of a schema used in some CreativeWork. For example, a document could declare a schemaVersion using an URL such as http://schema.org/version/2.0/ if precise indication of schema version was required by some application. http://schema.org/schemaVersion
version The version of the CreativeWork embodied by a specified resource. http://schema.org/version
video An embedded video object. http://schema.org/video
altLabel The alternate label. http://www.w3.org/2004/02/skos/core#altLabel
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

Activity

An assessment in a protocol.

URI: http://schema.repronim.org/Activity

Name Description URI
addProperties An array of objects to describe the various properties added to assessments and fields. http://schema.repronim.org/addProperties
allow An array of items indicating properties allowed on an activity or protocol http://schema.repronim.org/allow
compute An array of objects indicating computations in an activity or protocol and maps it to the corresponding Field 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. http://schema.repronim.org/compute
cronTable None http://schema.repronim.org/cronTable
messages An array of objects to define conditional messages in an activity or protocol. http://schema.repronim.org/messages
order An ordered list to describe the order in which the items of an assessment or protocol appear in the user interface. http://schema.repronim.org/order
overrideProperties An array of objects to override the various properties added to assessments and fields. http://schema.repronim.org/overrideProperties
preamble The preamble for an assessment http://schema.repronim.org/preamble
shuffle An element (bool) to determine if the list of items is shuffled or in order. http://schema.repronim.org/shuffle
about The subject matter of the Field. http://schema.org/about
audio An embedded audio object. http://schema.org/audio
citation A citation or reference to another creative work, such as another publication, web page, scholarly article, etc. http://schema.org/citation
description A description of the item. http://schema.org/description
image An image of the item. This can be a URL or a fully described ImageObject. http://schema.org/image
schemaVersion Indicates (by URL or string) a particular version of a schema used in some CreativeWork. For example, a document could declare a schemaVersion using an URL such as http://schema.org/version/2.0/ if precise indication of schema version was required by some application. http://schema.org/schemaVersion
version The version of the CreativeWork embodied by a specified resource. http://schema.org/version
video An embedded video object. http://schema.org/video
altLabel The alternate label. http://www.w3.org/2004/02/skos/core#altLabel
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

Field

An item in an assessment.

URI: http://schema.repronim.org/Field

Name Description URI
additionalNotesObj 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. http://schema.repronim.org/additionalNotesObj
inputType An element to describe the input type of a Field item. http://schema.repronim.org/inputType
preamble The preamble for an assessment http://schema.repronim.org/preamble
responseOptions An element (object or by URL)to describe the properties of response of the Field item. http://schema.repronim.org/responseOptions
about The subject matter of the Field. http://schema.org/about
audio An embedded audio object. http://schema.org/audio
description A description of the item. http://schema.org/description
image An image of the item. This can be a URL or a fully described ImageObject. http://schema.org/image
isPartOf Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. http://schema.org/isPartOf
question A sub property of object. A question. http://schema.org/question
readonlyValue Whether or not a property is mutable. Default is false. Specifying this for a property that also has a value makes it act similar to a "hidden" input in an HTML form. http://schema.org/readonlyValue
schemaVersion Indicates (by URL or string) a particular version of a schema used in some CreativeWork. For example, a document could declare a schemaVersion using an URL such as http://schema.org/version/2.0/ if precise indication of schema version was required by some application. http://schema.org/schemaVersion
version The version of the CreativeWork embodied by a specified resource. http://schema.org/version
video An embedded video object. http://schema.org/video
altLabel The alternate label. http://www.w3.org/2004/02/skos/core#altLabel
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

AdditionalProperty

An object to describe the various properties added to assessments and fields.

URI: http://schema.repronim.org/AdditionalProperty

Name Description URI
allow An array of items indicating properties allowed on an activity or protocol http://schema.repronim.org/allow
isAbout A pointer to the node describing the item. http://schema.repronim.org/isAbout
isVis An element to describe (by boolean or conditional statement) visibility conditions of items in an assessment. http://schema.repronim.org/isVis
limit An element to limit the duration (uses ISO 8601) this activity is allowed to be completed by once activity is available. http://schema.repronim.org/limit
maxRetakes Defines number of times the item is allowed to be redone. http://schema.repronim.org/maxRetakes
randomMaxDelay Present activity/item within some random offset of activity available time up to the maximum specified by this ISO 8601 duration http://schema.repronim.org/randomMaxDelay
schedule An element to set make activity available/repeat info using ISO 8601 repeating interval format. http://schema.repronim.org/schedule
variableName The name used to represent an item. http://schema.repronim.org/variableName
valueRequired Whether the property must be filled in to complete the action. Default is false. http://schema.org/valueRequired
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

OverrideProperty

An object to override the various properties added to assessments and fields.

URI: http://schema.repronim.org/OverrideProperty

Name Description URI
isAbout A pointer to the node describing the item. http://schema.repronim.org/isAbout
isVis An element to describe (by boolean or conditional statement) visibility conditions of items in an assessment. http://schema.repronim.org/isVis
limit An element to limit the duration (uses ISO 8601) this activity is allowed to be completed by once activity is available. http://schema.repronim.org/limit
maxRetakes Defines number of times the item is allowed to be redone. http://schema.repronim.org/maxRetakes
randomMaxDelay Present activity/item within some random offset of activity available time up to the maximum specified by this ISO 8601 duration http://schema.repronim.org/randomMaxDelay
schedule An element to set make activity available/repeat info using ISO 8601 repeating interval format. http://schema.repronim.org/schedule
variableName The name used to represent an item. http://schema.repronim.org/variableName
valueRequired Whether the property must be filled in to complete the action. Default is false. http://schema.org/valueRequired
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

UnitOption

An object to represent a human displayable name alongside the more formal value for units.

URI: http://schema.repronim.org/UnitOption

Name Description URI
value The value for each option in choices or in additionalNotesObj http://schema.repronim.org/value
prefLabel The preferred label. http://www.w3.org/2004/02/skos/core#prefLabel

ResponseOption

An element (object or by URL)to describe the properties of response of the Field item.

URI: http://schema.repronim.org/ResponseOption

Name Description URI
choices An array to list the available options for response of the Field item. http://schema.repronim.org/choices
datumType Indicates what type of datum the response is (e.g. range,count,scalar etc.) for the Field item. http://schema.repronim.org/datumType
multipleChoice Indicates (by bool) if response for the Field item has one or more answer. http://schema.repronim.org/multipleChoice
unitOptions A list of objects to represent a human displayable name alongside the more formal value for units. http://schema.repronim.org/unitOptions
valueType The type of the response of an item. For example, string, integer, etc. http://schema.repronim.org/valueType
maxValue The upper value of some characteristic or property. http://schema.org/maxValue
minValue The lower value of some characteristic or property. http://schema.org/minValue
unitCode The unit of measurement given using the UN/CEFACT Common Code (3 characters) or a URL. Other codes than the UN/CEFACT Common Code may be used with a prefix followed by a colon. http://schema.org/unitCode

Choice

An object to describe a response option.

URI: http://schema.repronim.org/Choice

Name Description URI
value The value for each option in choices or in additionalNotesObj http://schema.repronim.org/value
image An image of the item. This can be a URL or a fully described ImageObject. http://schema.org/image
name The name of the item. http://schema.org/name

ComputeSpecification

An object to define computations in an activity or protocol.

URI: http://schema.repronim.org/ComputeSpecification

Name Description URI
jsExpression A JavaScript expression to compute a score from other variables. http://schema.repronim.org/jsExpression
variableName The name used to represent an item. http://schema.repronim.org/variableName

MessageSpecification

An object to define messages in an activity or protocol.

URI: http://schema.repronim.org/MessageSpecification

Name Description URI
jsExpression A JavaScript expression to compute a score from other variables. http://schema.repronim.org/jsExpression
message The message to be conditionally displayed for an item. http://schema.repronim.org/message

AdditionalNoteObj

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

URI: http://schema.repronim.org/AdditionalNoteObj

Name Description URI
column An element to define the column name where the note was taken from. http://schema.repronim.org/column
source An element to define the source (eg. RedCap, NDA) where the note was taken from. http://schema.repronim.org/source
value The value for each option in choices or in additionalNotesObj http://schema.repronim.org/value

ResponseActivity

Captures information about some action that took place. It also links to information (entities) that were used during the activity

URI: http://schema.repronim.org/ResponseActivity

Name Description URI
endedAtTime None http://www.w3.org/ns/prov#endedAtTime
generated None http://www.w3.org/ns/prov#generated
startedAtTime None http://www.w3.org/ns/prov#startedAtTime
used None http://www.w3.org/ns/prov#used
wasAssociatedWith None http://www.w3.org/ns/prov#wasAssociatedWith
inLanguage The language of the content or performance or used in an action. Please use one of the language codes from the IETF BCP 47 standard. See also [[availableLanguage]]. http://schema.org/inLanguage

Response

Describes the response of an item.

URI: http://schema.repronim.org/Response

Name Description URI
wasAttributedTo None http://www.w3.org/ns/prov#wasAttributedTo
isAbout A pointer to the node describing the item. http://schema.repronim.org/isAbout
value The value for each option in choices or in additionalNotesObj http://schema.repronim.org/value

Participant

An Agent describing characteristics associated with a participant.

URI: http://schema.repronim.org/Participant

Name Description URI
subject_id The identifier of a participant http://purl.org/nidash/nidm#subject_id

SoftwareAgent

Captures information about some action that took place. It also links to information (entities) that were used during the activity

URI: http://schema.repronim.org/SoftwareAgent

Name Description URI
url URL of the item. http://schema.org/url
version The version of the CreativeWork embodied by a specified resource. http://schema.org/version