About¶

What is plugin-rosetta?¶

plugin-rosetta is a Python library for translating FHIR R4 clinical data into OMOP CDM 5.4 format. It is part of the plugin-healthcare ecosystem — a suite of composable, open-source data integration components for healthcare data engineering.

The name "rosetta" refers to the Rosetta Stone — the artefact that made it possible to translate between previously incompatible writing systems. plugin-rosetta plays an analogous role: it provides a transparent, standards-grounded translation layer between the two dominant healthcare data models in use today.

Design principles¶

Grounded in authoritative sources. OMOP schemas are generated directly from the OHDSI CommonDataModel CSV definitions. FHIR-to-OMOP field mappings are derived from the HL7 FHIR-OMOP Implementation Guide FML structure maps. Neither model is interpreted ad hoc.

Transparent and auditable. Both data models are expressed as LinkML schemas. The exact_mappings annotations in fhir_resources.yaml are machine-readable and link every mapped FHIR field to its OMOP counterpart. Data stewards can inspect the mappings directly in the schema files or on the Mappings page.

No black-box mapping framework. Translations are implemented as plain Python classes — one per FHIR resource — with no intermediate mapping DSL. The code is straightforward to read, test, and extend.

Three-layer validation. Output is validated at the columnar level (nyctea + Polars), the record level (Pydantic v2), and the semantic level (LinkML validate()).

Source pins¶

Contributing¶

Contributions are welcome. Please open an issue or pull request on GitHub.

See CONTRIBUTING.md for guidelines.

License¶

plugin-rosetta is released under the MIT License.