Convert-Pheno Documentation

Overview

Clinical and phenotypic data conversion across supported exchange models.

Convert-Pheno supports conversion routes involving BFF, PXF, OMOP-CDM, REDCap, cBioPortal, CDISC-ODM, CDISC Dataset-JSON, CDISC Dataset-XML, FHIR R4 and mCODE, CSV, and openEHR.

Run your first conversionChoose a conversionInstall

Project status

This documentation tracks Convert-Pheno 0.34.

The software is in active use and still evolving. Some conversion routes are more mature than others, so it is worth checking the format-specific pages before running a new conversion on real data.

Most users should use the CLI

The command-line interface is the main entry point for normal use. It supports real files, mapping files, REDCap dictionaries, OMOP tables, audit TSV files, and multi-entity BFF output.

The API and module interfaces are mainly for developers who need to call Convert-Pheno from another application or script.

Typical conversions

Most users come to Convert-Pheno for one of these tasks:

• convert PXF to BFF individuals, biosamples, datasets, and cohorts
• convert OMOP-CDM exports to BFF or PXF
• convert REDCap or CDISC-ODM data through a mapping file
• convert CDISC Dataset-JSON SDTM domains to BFF, PXF, or supported OMOP-CDM tables
• resolve CDISC Dataset-XML SDTM domains with Define-XML and convert them to BFF, PXF, or supported OMOP-CDM tables
• convert generic FHIR R4 or mCODE 4.0 Bundles to BFF, PXF, or supported OMOP-CDM tables
• convert cBioPortal clinical study packages to entity-aware BFF, PXF, or supported OMOP-CDM tables
• use mapped raw CSV as an ETL source for BFF, PXF, or supported OMOP-CDM tables
• convert BFF to PXF, flattened CSV, flattened JSON, or JSON-LD

Start Here

• 5-Minute Quickstart if you want to complete one small conversion now
• Choose a Conversion if you want a route finder and copy-paste commands for common conversions
• Supported Formats if you need accepted files and format-specific behavior

API vs CLI

Use the HTTP(s) API mainly for self-contained JSON payloads such as BFF, PXF, FHIR R4 Bundles, and carefully prepared OMOP-CDM requests.

For mapping-file-based conversions such as CSV, REDCap, and CDISC-ODM, or multi-file Dataset-JSON/Dataset-XML input, prefer the CLI.

Documentation map

• Command-Line Interface if you want to run the tool now
• Mapping Files for an end-to-end mapped REDCap workflow
• Use as an API if you want the HTTP(s) contract, API support matrix, and JavaScript fetch examples
• Troubleshooting if something is not behaving as expected
• Implementation if you want the architectural view

External components

• GitHub repository