Supported Formats

The summary below shows what Convert-Pheno can read and write. File requirements and format-specific options are covered by the Format Guides in the sidebar.

• Inputs: BFF, Phenopackets v2, OMOP-CDM, REDCap, cBioPortal clinical studies, CDISC-ODM, OpenClinica ODM exports, CDISC Dataset-JSON, CDISC Dataset-XML, FHIR R4 and mCODE Bundles, i2b2, PCORnet CDM, Sentinel CDM, CSV, and openEHR canonical compositions
• Main outputs: BFF, Phenopackets v2, and OMOP-CDM CSV tables
• Inspection outputs: flattened JSON or YAML, CSV, and JSON-LD or YAML-LD from BFF or PXF input

Most routes use BFF as the internal target model. The CLI handles any intermediate BFF conversion automatically.

Conversion map

Direct mapping steps around BFF, which can be the requested output or an internal intermediate. Any connected path through BFF runs as one CLI command: for example, Dataset-JSON to PXF performs Dataset-JSON to BFF and then BFF to PXF in memory. Dashed source borders mark implemented profiles with limited independent dataset coverage.

Additional outputs from BFF and PXF

For inspection and downstream processing, BFF and PXF input can also be written as flattened JSON or YAML, CSV, and JSON-LD or YAML-LD.

For runnable commands, continue to Choose a Conversion.