Skip to main content

Clinical data model conversion

Convert-Pheno

Conversion of clinical and phenotypic data between supported data models.

Open-source software for reproducible transformations among Beacon v2 Models, Phenopackets v2, OMOP-CDM, and supported clinical source formats. The command-line interface is the primary user interface; Perl, Python, and HTTP(s) interfaces are also available for integration.

Run Your First ConversionChoose a ConversionInstall
Supported input data models are converted by Convert-Pheno into a selected output data model

Conversion architecture

A common target model connects supported routes.

Most conversions normalize source records through Beacon v2 Models BFF before writing the output selected by the user.

Supported source families pass through Convert-Pheno and the Beacon v2 Models BFF target model to supported outputs
Source formats are grouped by function for readability. Route availability varies by input; see Supported Formats for the complete conversion map.

Current scope

Supported operations

Conversion behavior depends on the selected source and output route. Route-specific requirements are documented with the corresponding format.

Structured inputs

Convert supported models and exchange formats

Read BFF, PXF, OMOP-CDM, FHIR/mCODE, openEHR, cBioPortal, and CDISC dataset packages.

Mapped sources

Transform REDCap, CDISC-ODM/OpenClinica, and CSV

Use project mapping files to relate source fields to the target model.

Beacon entities

Write entity-aware BFF collections

Produce individuals, biosamples, datasets, and cohorts where the route supports them.

Auditability

Retain provenance and inspect searches

Preserve source fields and optionally record ontology lookup decisions.