CDISC COSMoS Qualified Biomedical Concepts (overlay)
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CDISC COSMoS Qualified Biomedical Concepts (overlay)

Release: 2026-09-01

Modified on: 2026-09-04
Revision:
v0.4.0
Authors:
Kerstin Forsberg
Imported Ontologies:
<https://w3id.org/cdisc/cosmos/bc/>
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://opensource.org/licenses/MIT
Cite as:
Forsberg, K. (2026). CDISC COSMoS Qualified Biomedical Concepts (overlay). https://w3id.org/cdisc/cosmos/qbc/
Provenance of this page
Ontology Specification Draft

CDISC COSMoS Qualified Biomedical Concepts (overlay): Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

CDISC COSMoS Qualified Biomedical Concepts (overlay): Description back to ToC

An authored overlay on the mechanical rendering of CDISC COSMoS: the qualified (sibling) biomedical concept, with an identity of its own, typed mappings to external code systems, a single result scale, an authoritative result data element concept, a concept-level semantic value set, and a state-keyed interpretation-regime assertion. Every term declared here is this repo's, not CDISC's; the terms it reuses keep the IRIs CDISC published. The concepts it qualifies are the ones cosmos_bc_v1.instances.ttl renders, reached by skos:broader.

Cross-reference for CDISC COSMoS Qualified Biomedical Concepts (overlay) classes, object properties and data properties back to ToC

This section provides details for each class and property defined by CDISC COSMoS Qualified Biomedical Concepts (overlay).

Classes

AssignedTermc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/AssignedTerm

Stand-in for cosmos_sdtm:AssignedTerm, declared locally because the SDTM model is not imported (D19). Attributes copied verbatim from cosmos_sdtm_model.yaml at the pinned commit. Measured 2026-09-01: gen-jsonld-context honours the class_uri and maps the term to cosmos_sdtm:AssignedTerm, while gen-owl mints qbc:AssignedTerm and demotes the published IRI to a skos:exactMatch. Both readings are kept; the divergence is the same one decisions D8 and D11 record for the core rendering. NOTE: conceptId and value are declared on more than one class in this schema, so gen-owl reports them ambiguous and emits bare property declarations with no range or pattern. gen-shacl keeps the per-class patterns apart. The warning is left in place - see D19; silencing it with slot_uri merges the definitions instead.
has super-classes
is in range of
specimen op

broadMatchc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/MappingRelationEnum#broadMatch

has super-classes
MappingRelationEnum c

ConceptTermc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/ConceptTerm

BC-side coded term: an NCIt concept with its preferred term. Used for the concept-level admissible specimen set; the SDTM submission value for the same concept lives on the recording's AssignedTerm.
has super-classes
is in range of
admissibleSpecimens op

exactMatchc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/MappingRelationEnum#exactMatch

has super-classes
MappingRelationEnum c

ExternalMappingc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/ExternalMapping

Typed mapping to an external code system. Replaces the flat cosmos_bc:Coding for siblings: cardinality 0/1/>1 is handled by the mapping relation, not by the key (exactMatch = same observable; narrowMatch = finer external leaf, typically the unit dimension).
has super-classes
is in range of
externalMappings op

InterpretationRegimeAssertionc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/InterpretationRegimeAssertion

Asserts that a distinct interpretation regime applies to this sibling under a given subject state. Carries a coded pointer, NEVER the reference-range numbers (those are data, per-record/per-lab). Keyed on an existing state DEC — for glucose, Fasting Status Indicator C93566 — so fasting and post-load glucose share one sibling while carrying different regimes.
has super-classes
is in range of
interpretationRegimes op

MappingRelationEnumc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/MappingRelationEnum

is equivalent to
broadMatch c or exactMatch c or narrowMatch c
has sub-classes
broadMatch c, exactMatch c, narrowMatch c

narrowMatchc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/MappingRelationEnum#narrowMatch

has super-classes
MappingRelationEnum c

QualifiedBiomedicalConceptc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/QualifiedBiomedicalConcept

A sibling BC: one observation shape under a broader analyte concept. Identity is the IRI itself (read-many, citable, content-negotiated per the usdm-rdf pattern). Deliberately NOT a subclass of cosmos_bc:BiomedicalConcept — see the design decision in the file header; the analyte link is skos:broader via broaderConceptId.
has super-classes

QualifiedBiomedicalConceptCollectionc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/QualifiedBiomedicalConceptCollection

Container for the instance file: the qualified concepts and their recordings. Exists so linkml-validate has a target class.
has super-classes

Recordingc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/Recording

Thinned SDTM dataset specialization: everything the sibling already states is inherited, not re-declared. Kept here: domain placement, topic/test code, the ONE specimen this recording uses, per-standard codelist bindings (incl. unit subset), origin, and an optional LOINC pin at recording grain. Dropped relative to cosmos_sdtm:SDTMGroup's variables: result dataType/length/ format/significantDigits (inherited via the sibling's result DEC — verified to introduce no contradiction), and the duplicated scale information.
has super-classes

ResultScalec back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/ResultScale

A result scale the overlay admits, anchored to NCIt. The node is the overlay's use of one permissible value of CDISC's BiomedicalConceptResultScaleEnum: the value keeps the core IRI (D20) and is reached by permissibleValue as an edge, and the typed mappings to the NCIt Scale branch are written here, never onto the CDISC value or the NCIt PURL (D21, D22). Three instances - Nominal, Ordinal, Quantitative - and no more: the other two values the enum carries, Temporal and Narrative, are data types by measurement (known-gaps 4a), get no node, and a qualified concept's resultScale must be one of the three. This is the repo's interim reading while the one-axis-or-two question is open with CDISC; if CDISC anchors the enum itself, these nodes become redundant and can go. Decision D23.
has super-classes

SemanticValueSetTermc back to ToC or Class ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/SemanticValueSetTerm

Concept-level admissible result value (what the observation can say), distinct from any per-standard codelist binding (how a given standard writes it). ncitCode absent when no concept exists yet. A value is never a "[VERIFY]" placeholder: where no set can be curated the slot is absent, and the renderer refuses a marker in the value position (D22).
has super-classes
is in range of
semanticValueSet op

Object Properties

admissibleSpecimensop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/admissibleSpecimens

Concept-level admissible specimen set (NCIt-coded)
has range
ConceptTerm c

externalMappingsop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/externalMappings

has range
ExternalMapping c

interpretationRegimesop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/interpretationRegimes

has range
InterpretationRegimeAssertion c

permissibleValueop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/permissibleValue

The CDISC permissible value this ResultScale node is the use of. Same range and same core-IRI resolution as resultScale (D20).
has range
Biomedical Concept Result Scale Enum c

qualifierDataElementConceptsop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/qualifierDataElementConcepts

has range
Data Element Concept c

recordingsop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/recordings

relationop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/relation

resultDataElementConceptop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/resultDataElementConcept

The result DEC with AUTHORITATIVE dataType; recordings inherit it (SDTMVariable.dataElementConceptId -> DEC.dataType), they do not re-declare it.
has range
Data Element Concept c

resultScaleop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/resultScale

Single scale of measurement — the sibling split axis. Ranges over CDISC's five-value enum unchanged (D20), but the identity rule component x system x scale only holds over Nominal, Ordinal and Quantitative: measured at the pin, Temporal and Narrative are predicted by the result DEC's dataType and never combine with a scale, so they are data types carried in the wrong enum. See known-gaps.md 4a. The overlay admits exactly the three that are scales - the ResultScale nodes of D23 - and 75_render_qbc refuses any other value.
has range
Biomedical Concept Result Scale Enum c

resultScalesop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/resultScales

semanticValueSetop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/semanticValueSet

has range
SemanticValueSetTerm c

siblingsop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/siblings

specimenop back to ToC or Object Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/specimen

The SDTM specimen assigned term this recording uses. It sits at a different grain from the qualified concept's admissibleSpecimens: that set is NCIt concept-level (Serum C13325, Plasma C13356), while SDTM CT carries composite submission values (SERUM OR PLASMA C105706). So a recording's specimen is not required to be a member of the admissible set, and 75_render_qbc reports membership per recording rather than asserting it. Measured 2026-09-02: 6 of 8 recordings use a member, 2 (HCV RNA) use the composite. D22.
has range
AssignedTerm c

Data Properties

broaderConceptIddp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/broaderConceptId

NCIt C-code of the analyte concept (skos:broader)
has range

codedp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/code

commentdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/comment

e.g. which axis the narrowMatch refines

domaindp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/domain

Stand-in for cosmos_sdtm:domain (D19), copied verbatim. Measured 2026-09-01: gen-jsonld-context honours the slot_uri; gen-owl drops it entirely and emits qbc:domain with no mapping back.
has range
string

iridp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/iri

has range
any U R I

loincPinsdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/loincPins

ncitCodedp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/ncitCode

preferredTermdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/preferredTerm

recordingIddp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/recordingId

has range

regimedp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/regime

Coded pointer to the regime, in a governed regime vocabulary. NOT required, and populated nowhere: no such vocabulary exists, and inventing a URI to fill the slot would be the one fabricated identifier in the whole repo. What the assertion can say without it is still the ask — that this concept has a distinct interpretation regime under this subject state, and a different one under that state. Decision D15.

resultCodelistBindingdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/resultCodelistBinding

Per-standard result binding for Coded scales

siblingIridp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/siblingIri

has range
any U R I

stateDataElementConceptIddp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/stateDataElementConceptId

The state DEC this regime keys on (e.g. C93566)

stateValuedp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/stateValue

Value of the state under which this regime applies (from the state DEC's value domain, e.g. Y / N; "*" = any state).

systemdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/system

Code system URI (e.g. https://loinc.org/, NCIt)

testCodedp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/testCode

unitCodelistBindingdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/unitCodelistBinding

Per-standard unit binding (codelist / subset ref)

variableOverridesdp back to ToC or Data Property ToC

IRI: https://w3id.org/cdisc/cosmos/qbc/variableOverrides

Residual SDTM-specific variable content

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.