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2898 lines (2795 loc) · 95.2 KB
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id: https://w3id.org/dds
name: data-definition-spec
title: Data Definition Specification (DDS)
description: >-
Standards-agnostic canonical model for clinical data meaning, structure, and
governance. Projects to CDISC (SDTM/ADaM/Define-XML), FHIR, OMOP, and SDMX.
ODM/Define-XML is one serialization facet applied by the output generator;
the canonical model is not ODM-derived.
license: MIT
prefixes:
linkml: https://w3id.org/linkml/
skos: http://www.w3.org/2004/02/skos/core#
odm: https://cdisc.org/odm2/
usdm: https://cdisc.org/usdm/
sdtm: https://cdisc.org/cosmos/sdtm_v1.0#
fhir: http://hl7.org/fhir/
ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
omop: https://omop.org/omop-cdm/
qb: http://purl.org/linked-data/cube#
sdmx: http://purl.org/linked-data/sdmx#
dprod: https://ekgf.github.io/dprod/
prov: http://www.w3.org/ns/prov#
dcat: http://www.w3.org/ns/dcat#
odrl: http://www.w3.org/ns/odrl/2/
osb: https://openstudybuilder.com/
dcterms: http://purl.org/dc/terms/
dds: https://w3id.org/dds/
default_prefix: dds
default_range: string
imports:
- linkml:types
classes:
IdentifiableElement:
abstract: true
mixins:
- Identifiable
- Labelled
GovernedElement:
abstract: true
mixins:
- Identifiable
- Labelled
- Governed
slot_usage:
OID:
required: true
Identifiable:
description: >-
A mixin that provides slots for making an entity addressable within a study or context
mixin: true
attributes:
OID:
description: >-
Local identifier within this study/context.
Use CDISC OID format for regulatory submissions,
or simple strings for internal use.
identifier: true
required: false
uuid:
description: Universal unique identifier
Governed:
description: >-
A mixin that provides slots for audit trail and standards governance, including mandatory status, comments, and attribution
mixin: true
attributes:
mandatory:
description: >-
Is this element required?
range: boolean
comments:
description: >-
Comment on the element, such as a rationale for its inclusion or exclusion
range: Comment
multivalued: true
inlined: false
siteOrSponsorComments:
description: >-
Comment on the element, such as a rationale for its inclusion or exclusion
range: SiteOrSponsorComment
multivalued: true
inlined: false
purpose:
description: Purpose or rationale for this data element
any_of:
- range: string
- range: TranslatedText
lastUpdated:
description: When the resource was last updated
range: datetime
owner:
description: Party responsible for this element
exact_mappings:
- prov:wasAttributedTo
any_of:
- range: User
- range: Organization
- range: string
wasDerivedFrom:
description: >-
Reference to another item that this item implements or extends, e.g. a template Item definition.
exact_mappings:
- prov:wasDerivedFrom
any_of:
- range: Item
- range: ItemGroup
- range: Specification
- range: CodeList
- range: Concept
- range: ConceptProperty
- range: LogicalPredicate
- range: Method
- range: Dataflow
- range: CubeComponent
- range: DataProduct
- range: ProvisionAgreement
Labelled:
description: >-
A mixin that provides slots for detailing meanings and multilingual descriptions
mixin: true
attributes:
name:
description: Short name or identifier, used for field names
description:
description: Detailed description, shown in tooltips
any_of:
- range: string
- range: TranslatedText
coding:
description: Semantic tags for this element
range: Coding
multivalued: true
inlined: true
inlined_as_list: true
label:
description: Human-readable label, shown in UIs
any_of:
- range: string
- range: TranslatedText
exact_mappings:
- skos:prefLabel
aliases:
description: >-
Alternative name or identifier
any_of:
- range: string
- range: TranslatedText
multivalued: true
inlined: true
inlined_as_list: true
exact_mappings:
- skos:altLabel
Formatted:
description: >-
A mixin that provides slots for reporting, exchange, or storage formatting
mixin: true
related_mappings:
- sdmx:Facet
- sdmx:Representation
attributes:
decimalDigits:
description: >-
For decimal values, the number of digits after the decimal point
range: integer
displayFormat:
description: >-
A display format for the item
significantDigits:
description: >-
For numeric values, the number of significant digits
range: integer
Versioned:
description: >-
A mixin that provides version and connectivity information, including version numbers and resource references
mixin: true
attributes:
version:
description: >-
The version of the external resources
href:
description: Machine-readable instructions to obtain the resource e.g. FHIR path, URL
required: false
IsProfile:
description: >-
A mixin that provides additional metadata for FHIR resources and Data Products, including profiles, security tags, and validity periods
mixin: true
mixins:
- Versioned
attributes:
profile:
description: Profiles this resource claims to conform to
multivalued: true
security:
description: Security tags applied to this resource
range: Coding
multivalued: true
inlined: true
inlined_as_list: true
authenticator:
description: Who/what authenticated the resource
any_of:
- range: User
- range: Organization
- range: string
required: false
validityPeriod:
description: Time period during which the resource is valid
range: Timing
required: false
ODMItemSerialization:
mixin: true
description: >-
A mixin providing ODM/CDISC-specific item attributes meaningful only in
ODM/Define-XML serialization: CRF completion instructions, CDISC notes,
implementation notes, collection exception predicates, and pre-specified
values. Applied by the ODM output generator. Not part of the canonical Item.
attributes:
role:
description: >-
Identifies the role of the item within the containing context, taken from the roleCodeList
any_of:
- range: string
- range: TranslatedText
roleCodeList:
description: >-
Reference to the CodeList that defines the roles for this item
range: CodeList
hasNoData:
description: >-
True if this is a manifest and there is no data for this item
range: boolean
crfCompletionInstructions:
any_of:
- range: string
- range: TranslatedText
description: >-
CRFCompletionInstructions reference: Instructions for the clinical site on how to enter collected information on the CRF
cdiscNotes:
any_of:
- range: string
- range: TranslatedText
description: >-
CDISCNotes reference: Explanatory text for the variable
implementationNotes:
description: >-
ImplementationNotes reference: Further information, such as rationale and implementation instructions, on how to implement the CRF data collection fields
any_of:
- range: string
- range: TranslatedText
collectionExceptionPredicate:
description: >-
Logical predicate defining when data collection for this item may be exempted.
range: LogicalPredicate
preSpecifiedValue:
description: >-
Prefill value or a default value for a field that is automatically populated.
any_of:
- range: string
- range: TranslatedText
ODMStandardReference:
description: >-
A mixin providing attributes for CDISC standards compliance indication.
Applied when serializing to Define-XML context. Not canonical.
mixin: true
attributes:
standard:
description: Reference to the standard being implemented
range: Standard
isNonStandard:
description: One or more members of this set are non-standard extensions
range: boolean
ODMSerializationMetadata:
description: >-
A mixin providing ODM/Define-XML file-level attributes required only when
serializing to ODM or Define-XML format. Applied by the ODM output generator,
not by the canonical model itself. These attributes (fileOID, odmVersion,
defineVersion, etc.) have no meaning in FHIR, OMOP, or SDMX projections.
mixin: true
attributes:
fileOID:
description: Unique identifier for the ODM file
required: true
asOfDateTime:
description: Date and time when the data snapshot was taken
range: datetime
creationDateTime:
description: Date and time when the ODM file was created
range: datetime
required: true
odmVersion:
description: Version of the ODM standard used
required: true
fileType:
description: Type of ODM file (e.g., Snapshot, Transactional)
required: true
originator:
description: Organization or system that created the ODM file
sourceSystem:
description: Source system that generated the data
sourceSystemVersion:
description: Version of the source system
context:
description: Define-XML context (usually "Other" for Define-XML)
defineVersion:
description: Version of Define-XML specification used
StudyMetadata:
description: >-
A mixin that provides study-level metadata attributes including study identification and protocol information
mixin: true
attributes:
studyOID:
description: Unique identifier for the study
required: true
studyName:
description: Name of the study
studyDescription:
description: Description of the study
protocolName:
description: Protocol name for the study
Specification:
tree_root: true
description: >-
The root specification container: a versioned, governed definition of the
data model for a study or data product. Links items, item groups, methods,
code lists, concepts, and study design references. Projects to Define-XML
MetaDataVersion, FHIR ImplementationGuide, and OMOP CDM metadata.
ODMSerializationMetadata is applied by the ODM output generator, not here.
close_mappings:
- usdm:StudyDesign
related_mappings:
- fhir:ImplementationGuide
- omop:cdm_source
is_a: GovernedElement
mixins:
- StudyMetadata
attributes:
itemGroups:
description: >-
Item groups, containing items, defined in this version of the metadata
range: ItemGroup
multivalued: true
inlined: true
inlined_as_list: true
items:
description: >-
Template or top-level items (not belonging to any item group) defined in this version of the metadata
range: Item
multivalued: true
inlined: true
inlined_as_list: true
predicates:
description: >-
Reusable logical predicates defined in this specification.
range: LogicalPredicate
multivalued: true
inlined: true
inlined_as_list: true
applicabilityConditions:
description: >-
Named applicability conditions defined in this specification.
range: ApplicabilityCondition
multivalued: true
inlined: true
inlined_as_list: true
methods:
description: >-
Methods defined in this version of the metadata.
range: Method
multivalued: true
inlined: true
inlined_as_list: true
analyses:
description: >-
Analyses defined in this version of the metadata.
range: Analysis
multivalued: true
inlined: true
inlined_as_list: true
codeLists:
description: >-
Code lists defined in this version of the metadata.
range: CodeList
multivalued: true
inlined: true
inlined_as_list: true
codings:
description: Codings defined in this version of the metadata
range: Coding
multivalued: true
inlined: true
inlined_as_list: true
concepts:
description: Structured Concepts defined in this version of the metadata
range: Concept
multivalued: true
relationships:
description: >-
Relationships between items, item groups, and other elements in this version of the metadata.
range: Relationship
multivalued: true
inlined: true
inlined_as_list: true
queries:
description: >-
Queries raised against metadata and/or data elements in this specification.
Each Query references its target element(s) by OID, so the same query can
relate to many metadata and data elements (many-to-many).
range: Query
multivalued: true
inlined: true
inlined_as_list: true
checks:
description: >-
Reusable validation checks (e.g. published CORE rules) included in this
metadata package. Each Check references the elements it applies to by OID
and may cite an external published rule, enabling reuse and loose coupling.
range: Check
multivalued: true
inlined: true
inlined_as_list: true
dictionaries:
description: Dictionaries defined in this version of the metadata
range: Dictionary
multivalued: true
inlined: true
inlined_as_list: true
standards:
description: >-
Standards defined in this version of the metadata
range: Standard
multivalued: true
inlined: true
inlined_as_list: true
annotatedCRFs:
description: >-
Reference to annotated case report forms
range: DocumentReference
multivalued: true
inlined: true
inlined_as_list: true
resources:
description: >-
References to resources and documents that describe this version of the metadata.
any_of:
- range: DocumentReference
- range: Resource
multivalued: true
inlined: true
inlined_as_list: true
dataProducts:
description: >-
Indexed data flows with clear ownership
range: DataProduct
multivalued: true
inlined: true
inlined_as_list: true
displays:
description: >-
Displays defined in this version of the metadata.
range: Display
multivalued: true
inlined: true
inlined_as_list: true
usdmStudyDesignId:
description: >-
OID or URI reference to the USDM StudyDesign that this specification
implements. When present, arms, epochs, and scheduled visit slots are
resolved from the referenced USDM instance. The USDM study design is the
authoritative source for EPOCH, VISITNUM, ARM, and timing anchors; DDS
does not redeclare them.
required: false
Item:
description: >-
A data element that represents a specific piece of information within a defined context, with data type, constraints, and derivation methods
close_mappings:
- odm:ItemRef
- odm:ItemDef
- qb:ComponentSpecification
- sdmx:DataAttribute
- sdmx:MetadataAttribute
narrow_mappings:
- fhir:StructureDefinition/variable
- fhir:Questionnaire/item
- qb:ComponentProperty
- omop:Field
- omop:DerivedColumn
related_mappings:
- usdm:BiomedicalConceptProperty
- usdm:DerivationConceptProperty
- usdm:AnalysisConceptProperty
- fhir:ElementDefinition
- qb:MeasureProperty
- qb:AttributeProperty
- sdmx:Concept
- sdmx:Component
- sdmx:Representation
- osb:sdtm_variable
- osb:specimen
- osb:unit_dimension
- osb:std_unit
is_a: GovernedElement
mixins:
- Formatted
# ODMItemSerialization is applied by the ODM output generator, not here.
attributes:
dataType:
description: >-
The data type of the item.
range: DataType
required: true
length:
description: >-
The maximum length of the data item in characters.
range: integer
codeList:
description: >-
Reference to the CodeList that constrains the item values.
range: CodeList
method:
description: >-
Reference to the Method element that describes how to derive this item's value.
range: Method
rangeChecks:
description: Range checks applied to this item (e.g. edit checks, CORE rules)
range: RangeCheck
multivalued: true
inlined: true
inlined_as_list: true
applicableWhen:
description: |
References to different situations that define when this item applies.
Multiple applicabilityConditions are combined with OR logic: the item applies if ANY referenced ApplicabilityCondition matches.
Within each ApplicabilityCondition, conditions are combined with AND logic: all conditions must be true.
Example: whereClause: ["WC.SYSBP", "WC.DIABP"] means the item applies when
(all conditions in WC.SYSBP are true) OR (all conditions in WC.DIABP are true).
range: ApplicabilityCondition
multivalued: true
inlined: false
close_mappings:
- fhir:StructureDefinition/context
origin:
description: >-
The origin of the data
range: Origin
inlined: true
conceptProperty:
description: >-
Reference to a abstract concept property that this item is a specialization / instance of.
range: ConceptProperty
ItemGroup:
description: >-
A collection element that groups related items or subgroups within a specific context, used for tables, FHIR resource profiles, biomedical concept specializations, or form sections
close_mappings:
- odm:ItemGroupDef
- odm:ItemGroupRef
- osb:ActivityInstance
narrow_mappings:
- fhir:StructureDefinition
- fhir:ViewDefinition
- fhir:Questionnaire
- omop:Table
- qb:DataStructureDefinition
- sdmx:DataStructureDefinition
related_mappings:
- qb:DataSet
- qb:Observation
- qb:ObservationGroup
- qb:Slice
- osb:Activity
is_a: GovernedElement
mixins:
- IsProfile
- ODMStandardReference
attributes:
domain:
description: >-
Domain abbreviation for the dataset.
structure:
description: >-
Data structure of the item group, indicating how the records are organized.
If this is a FHIR Resource, is it nested or flattened?
If this is a structured concept, is it a Biomedical/Derivation/Analysis concept?
any_of:
- range: string
- range: TranslatedText
isReferenceData:
description: >-
Set to Yes if this is a reference item group.
range: boolean
type:
description: >-
Type of item group
range: ItemGroupType
items:
description: Items in this group
range: Item
multivalued: true
close_mappings:
- fhir:StructureDefinition/snapshot
- fhir:StructureDefinition/differential
inlined: true
inlined_as_list: true
uniqueKey:
description: >-
Unordered set of Items whose combined values uniquely identify a record in
this dataset (the record key). Each entry is an OID reference to an Item in
the items array. Order is not significant for uniqueness — use keySequence
for sort order. Splitting uniqueness from sorting resolves the previous
overloading of keySequence.
range: Item
multivalued: true
close_mappings:
- odm:ItemRef.KeySequence
keySequence:
description: >-
Ordered list of Items defining the default sort order for this dataset.
Each entry is an OID reference to an Item in the items array; order
determines sorting precedence and merge operations. May reference Items
that are not part of uniqueKey. Distinct from uniqueKey, which establishes
record uniqueness.
range: Item
multivalued: true
close_mappings:
- sdmx:DimensionDescriptor
slices:
description: >-
Slices are specific subset ItemGroups that belong to, or are used by this ItemGroup
range: ItemGroup
multivalued: true
inlined: true
inlined_as_list: true
implementsConcept:
description: >-
Reference to a abstract concept topic that this item group is a specialization of
range: Concept
applicableWhen:
description: |
References to different situations that define when this item applies.
Multiple applicabilityConditions are combined with OR logic: the item applies if ANY referenced ApplicabilityCondition matches.
Within each ApplicabilityCondition, conditions are combined with AND logic: all conditions must be true.
Example: whereClause: ["WC.SYSBP", "WC.DIABP"] means the item applies when
(all conditions in WC.SYSBP are true) OR (all conditions in WC.DIABP are true).
range: ApplicabilityCondition
multivalued: true
inlined: false
close_mappings:
- fhir:StructureDefinition/context
hasNoData:
description: >-
Used to indicate that this ItemGroup has no data, e.g. for a manifest.
range: boolean
observationClass:
description: >-
Identifies the predefined CDISC model Class.
range: DefClass
required: false
DefClass:
description: >-
The predefined CDISC model Class that applies to an ItemGroupDef.
attributes:
name:
description: >-
Name of the General Observation Class following CDISC Controlled Terminology.
required: true
subClasses:
description: >-
One or more SubClasses that further identify the specific SubClass within a Class.
range: SubClass
multivalued: true
required: false
inlined: true
inlined_as_list: true
SubClass:
description: >-
A specific SubClass within a CDISC model Class.
attributes:
name:
description: >-
Name of the SubClass following CDISC Controlled Terminology for SubClass.
required: true
parentClass:
description: >-
Name of the parent Class or SubClass following CDISC Controlled Terminology.
required: false
subClasses:
description: >-
Nested SubClass(es) for multi-level SubClass hierarchy.
range: SubClass
multivalued: true
required: false
inlined: true
inlined_as_list: true
Relationship:
description: >-
A semantic link that defines connections between elements such as Items or ItemGroups, capturing relationships like "is the unit for" or "assesses seriousness of"
from_schema: sdtm
related_mappings:
- sdmx:ConceptSchemeMap
is_a: IdentifiableElement
attributes:
subject:
description: >-
The starting element of the relationship (e.g., an Item or ItemGroup).
range: IdentifiableElement
required: true
object:
description: >-
The ending element of the relationship.
range: IdentifiableElement
required: true
predicateTerm:
description: >-
Short variable relationship linking phrase for programming purposes.
range: PredicateTermEnum
required: true
linkingPhrase:
description: >-
Variable relationship descriptive linking phrase.
range: LinkingPhraseEnum
required: true
Query:
description: >-
A reified query (discrepancy, request for clarification, or annotation) raised
against one or more metadata and/or data elements. Modelled as an intermediate
relationship node so a single query can relate to many elements (many-to-many)
and be referenced rather than embedded. Internal queries originate within the
organization; external queries (e.g. site or sponsor) carry their source.
close_mappings:
- odm:Query
is_a: GovernedElement
attributes:
about:
description: >-
The metadata and/or data element(s) this query concerns, referenced by OID.
Multivalued and non-inlined to support many-to-many linkage across both
metadata (e.g. Item, ItemGroup) and data (e.g. Dataset) elements.
range: IdentifiableElement
multivalued: true
inlined: false
required: true
queryType:
description: >-
Whether the query is internal or external (e.g. site or sponsor originated).
range: QueryType
text:
description: The query content.
any_of:
- range: string
- range: TranslatedText
required: true
status:
description: Workflow status of the query (e.g. open, answered, closed).
source:
description: The party that raised the query.
any_of:
- range: User
- range: Organization
- range: string
Translation:
description: >-
A text representation that provides content in a specific language, used for multilingual support
exact_mappings:
- odm:TranslatedText
- sdmx:LocalisedString
attributes:
"language":
description: The language of the translation
required: true
"value":
description: The translated text
required: true
TranslatedText:
description: >-
A container of the language-specific translations of a single piece of text
(a set of localised strings), as opposed to one Translation.
exact_mappings:
- sdmx:InternationalString
attributes:
translations:
range: Translation
multivalued: true
inlined: true
inlined_as_list: true
CodeList:
description: >-
A value set that defines a discrete collection of permissible values for an item, corresponding to the ODM CodeList construct
exact_mappings:
- odm:CodeList
- fhir:ValueSet
close_mappings:
- skos:Collection
- sdmx:ItemScheme
- qb:codeList
related_mappings:
- usdm:BiomedicalConceptProperty/responseCodes
narrow_mappings:
- sdmx:Codelist
- sdmx:ValueList
is_a: GovernedElement
mixins:
- Versioned
- ODMStandardReference
attributes:
dataType:
description: >-
The data type for the values in the code list
range: DataType
formatName:
description: >-
Name of a standard format definition
codeListItems:
description: >-
The individual values that make up this CodeList.
The type of CodeListItem included determines its behaviour
range: CodeListItem
multivalued: true
inlined: true
inlined_as_list: true
externalCodeList:
description: >-
Reference to a code list that is defined externally to this study
range: Resource
CodeListItem:
description: >-
A structured member of a CodeList that extends the Coding class with additional context-specific properties
exact_mappings:
- odm:CodeListItem
close_mappings:
- usdm:AliasCode
- usdm:ResponseCode
- fhir:CodeableConcept
- omop:Concept
narrow_mappings:
- sdmx:Code
- sdmx:ValueItem
attributes:
codedValue:
description: >-
The value of the CodeListItem before decoding
required: true
decode:
description: >-
The decoded value of the CodeListItem
description:
description: >-
A detailed description of the code (e.g., for documentation purposes)
any_of:
- range: string
- range: TranslatedText
coding:
description: >-
The dictionary definition of the CodeListItem
range: Coding
inlined: true
aliases:
description: Alternative labels for the code (ODM Alias, skos:altLabel)
any_of:
- range: string
- range: TranslatedText
multivalued: true
weight:
description: Numeric significance of the code (e.g., for scoring)
range: decimal
other:
description: >-
Flag to indicate that the term represents "other" content
range: boolean
Comment:
description: >-
A descriptive element that contains explanatory text provided by a data or metadata handler
exact_mappings:
- odm:CommentDef
- usdm:CommentAnnotation
- fhir:Annotation
- sdmx:Annotation
is_a: GovernedElement
attributes:
text:
description: >-
The comment text.
any_of:
- range: string
- range: TranslatedText
required: true
documents:
description: >-
References to documents that contain or are referenced by this comment
range: DocumentReference
multivalued: true
inlined: true
inlined_as_list: true
Coding:
description: >-
A semantic reference that provides standardized codes and their meanings from controlled vocabularies
exact_mappings:
- odm:Coding
- usdm:Code
- fhir:Coding
close_mappings:
- omop:Concept
- skos:Concept
- sdmx:Code
- sdmx:Concept
- sdmx:ISOConceptReference
attributes:
code:
description: >-
The code value
required: true
decode:
description: Human-readable meaning
any_of:
- range: string
- range: TranslatedText
exact_mappings:
- skos:prefLabel
codeSystem:
description: >-
The code system identifier
required: true
codeSystemVersion:
description: >-
The code system version
aliasType:
description: >-
How this coding is related in the context of its parent element
range: AliasPredicate
Dictionary:
description: >-
A dictionary that defines a set of codes and their meanings
close_mappings:
- omop:Vocabulary
- fhir:CodeSystem
- skos:ConceptScheme
- sdmx:ConceptScheme
is_a: IdentifiableElement
mixins:
- Versioned
attributes:
terms:
description: Terms in this dictionary - leave this empty in most cases to keep the file small
range: Coding
multivalued: true
inlined: true
inlined_as_list: true
publishedBy:
description: >-
Associates the Data Provider that reports/publishes the data.
any_of:
- range: Organization
- range: string
Concept:
description: >-
An abstract concept that can be referenced and specialised by data
implementations. Holds ConceptProperties describing the concept's expected
data shape. Multiple ItemGroups or Items can implement the same Concept,
allowing standard biomedical concepts to be implemented differently across
studies while remaining semantically aligned.
This is a structural concept definition (an SDMX MetadataStructureDefinition-style
shape that implementations conform to), not an ItemScheme/SKOS concept item. It
references a concept (sdmx:Concept / skos:Concept) but is not itself one; see
Coding for the vocabulary-item mapping.
close_mappings:
- sdmx:MetadataStructureDefinition
- osb:Activity
narrow_mappings:
- usdm:BiomedicalConcept
- usdm:AnalysisConcept
- usdm:DerivationConcept
related_mappings: