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Convert-Pheno Documentation

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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

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
  • 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

Documentation map

  • Use if you want to run the tool now
  • Tutorial if you want short guided 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