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Convert-Pheno Documentation

Convert-Pheno is a toolkit for converting clinical and phenotypic data between supported exchange models such as BFF, PXF, OMOP-CDM, REDCap, CDISC-ODM, and mapped CSV.

Project status

This documentation tracks Convert-Pheno 0.31.

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 workflow in production.

Get started See supported formats Install the toolkit

Typical workflows

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 raw CSV data through a mapping file
  • convert BFF to PXF, flattened CSV, flattened JSON, or JSON-LD

API vs CLI

Use the HTTP API mainly for self-contained JSON payloads such as BFF, PXF, and carefully prepared OMOP-CDM requests.

For mapping-file-based workflows such as CSV, REDCap, and CDISC-ODM, prefer the CLI.

Documentation map

  • Use if you want to run the tool now
  • Tutorial if you want short guided examples
  • Use as an API if you want the HTTP contract, API support matrix, and JavaScript fetch examples
  • Analysis if you want to work with the generated individuals.json
  • Troubleshooting if something is not behaving as expected
  • Implementation if you want the architectural view

External components