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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. Use the command line for scripts and larger workflows, or the native desktop application for interactive conversions with the same engine. Perl, Python and HTTP(s) interfaces are also available for integration.

Run Your First ConversionCommand-Line InterfaceDesktop App

Install locally · Try in Colab · Video tutorials

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, CDISC datasets, and supported clinical table exports.

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.