v2.0.3

v2.0.3 — Release Notes

Code System Version Updates

All ontology and code system versions have been updated to their latest
releases as reported by BioPortal:

Code System	Previous Version	Updated Version
SNOMEDCT	SNOMEDCT_US_2024_09_01	2025AB
LOINC	LNC278	281
HP	2025-05-06	2026-02-16
NCIT	24.01e	26.02d
NCBITAXON	NCBI2024_04_02	2025_04_10
GENO	2023-10-08	2026-02-02
UO	2023-05-25	2026-01-16
ECO	2025-06-23	releases/2025-06-23
ICD10CM	ICD10CM_2025	2026
MONDO	2025-06-03	2026-03-03
ORDO	4.7	4.8

Data Element Update: Sex at Birth (2.2)

The code for data element 2.2 Sex at Birth has been updated. The previous
SNOMED CT concept 281053000 | Sex of baby at delivery (observable entity)
was identified as inactive (deprecated). The element is now coded using
LOINC 76689-9 — Sex assigned at birth, aligning with HL7 FHIR's
Patient resource. Value set choices remain SNOMED CT encoded.

Repository and Package Structure Refactor

The versioned folder structure inside src/rd_cdm/instances/ has been removed.
Previously each release occupied a dedicated subdirectory (e.g. instances/v2_0_2/)
with the version repeated in filenames. Git tags and PyPI versioning already
serve as the version archive, making this redundant.

New flat structure:

src/rd_cdm/instances/
├── code_systems.yaml
├── data_elements.yaml
├── value_sets.yaml
├── rd_cdm.yaml          ← merged, version-stamped
├── jsons/rd_cdm.json
└── csvs/rd_cdm.csv

The data model version is now embedded directly in every exported file via
rd_cdm_version and rd_cdm_date fields, making all outputs self-describing.
To use an older version: pip install rd-cdm==2.0.2.

CLI Naming Update

All CLI commands renamed from rdcdm-* to rd-cdm-* for consistency with
the PyPI package name:

Old	New
rdcdm-merge	rd-cdm-merge
rdcdm-json	rd-cdm-json
rdcdm-csv	rd-cdm-csv
rdcdm-validate	rd-cdm-validate

The --version / -v argument has been removed from all CLI tools.

Validation Improvements

• Progress bars (via tqdm) added to rd-cdm-validate for all three phases
• Validation summary now reports the data model version
• Obsolete/deprecated term detection via BioPortal obsolete field

Dependency Changes

• Removed: numpy, requests-cache, jsonschema, oaklib
• Moved to dev extra: linkml (only needed to regenerate Python classes)
• Added: tqdm for validation progress reporting

Install with dev tools: pip install rd-cdm[dev]

Python Class Generation

gen_pydantic.py now generates both output files in a single run:

• rd_cdm.py — LinkML runtime dataclasses (via PythonGenerator)
• rd_cdm_pydantic.py — Pydantic v2 models (via PydanticGenerator)

---

What's Changed

• updated forms to v2-0-2 by @aslgraefe in #49
• 51 make release203 by @aslgraefe in #52
• Make Release/2.0.3 by @aslgraefe in #53

Full Changelog: v2.0.2...v2.0.3