Convert-Pheno Documentation

Overview

Clinical and phenotypic data conversion across supported exchange models.

Convert-Pheno converts between BFF, PXF, OMOP-CDM, REDCap, CDISC-ODM, mapped CSV, and related inspection formats.

What it doesWays to run itConversion recipes

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

Start Here

• Ways to Run Convert-Pheno if you are deciding between CLI, API, module, and Web App usage
• Conversion Recipes if you want copy-paste commands for common conversions
• Output Validation if you need to inspect provenance, audit ontology search, or validate output

API vs CLI

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

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

Documentation map

• Command-Line Interface if you want to run the tool now
• Tutorial if you want short guided examples
• Use as an API if you want the HTTP(s) 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

• Web App UI for display and exploration only; it currently runs an older Convert-Pheno version than this documentation
• GitHub repository