How BiomedicalConceptProperty values are generated in v1.4

[pendingintent]

This discussion documents the BiomedicalConceptProperty (BCP) generation workflow as resolved in issue #218 and implemented in v1.4.

Source of Property Data

BCPs are populated from two alternative sources depending on whether a SDTM Dataset Specialization (DSS) is associated with the Biomedical Concept:

SDTM path (preferred): When the user has associated a DSS with a BC, the generator iterates the DSS variables[] array and creates one BCP for each variable that:

1. Has a dataElementConceptId linking it to a specific Data Element Concept (DEC) in the BC
2. Passes the operational variable exclusion filter (see below)

Generic path (fallback): When no DSS is associated, the generator iterates the BCs dataElementConcepts[]` array directly, creating one BCP per DEC.

Operational Variable Exclusion List

The exclusion list is based on the reference implementation by Dave Iberson-Hurst in usdm_excel/cdisc_bc_library.py (_process_property method). Variables whose suffix (after the 2-character domain prefix) appears in this list are not included as BCPs:

TEST, STRESN, STRESU, STRESC, CLASCD, LOINC, LOT, CAT, SCAT,
LLT, LLTCD, HLT, HLTCD, PTCD, BODSYS, BDSYCD, SOC, SOCCD, RLDEV

The variable name EPOCH is also excluded unconditionally.

These are operational SDTM variables that carry derived, standardized, or classification values — not the conceptual properties of the measurement itself.

BCP Attribute Mapping

USDM BCP attribute	Source
name	SDTM variable name (SDTM path) or DEC shortName (generic path)
label	Same as name
isRequired	mandatoryValue from DSS variable (SDTM path) or True (generic path)
isEnabled	Always True
datatype	DSS variable dataType first, then DEC dataType (SDTM); DEC dataType (generic)
code.standardCode.code	DEC conceptId (NCIT C-code)
code.standardCode.codeSystem	http://www.cdisc.org
code.standardCode.codeSystemVersion	Package date from parentPackage href
code.standardCode.decode	DEC shortName
responseCodes	From DSS variable assignedTerm (when conceptId and value both present)

Key Design Decisions

• DSS variables without a matching DEC are skipped. Variables like LBTESTCD that identify the test (pointing back to the BC itself) are intentionally excluded. Only variables that reference a distinct DEC — representing an independent conceptual property — become BCPs.
• DSS dataType takes priority over DEC dataType. The specialization can specify a more precise numeric type (e.g., float) than the BCs generic DEC (e.g., string). This follows Daves reference implementation.
• isRequired reflects mandatoryValue. Unlike the reference implementation (which hardcodes True), the workbench preserves the distinction between mandatory and optional properties from the SDTM specialization.

Validation

The implementation is covered by tests/test_generate_biomedical_concept_properties.py (23 tests) including explicit assertions that the exclusion list matches the reference implementation in cdisc_bc_library.py.

Related discussions resolved: #147, #196, #209
Implementation issue: #218