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, i2b2, PCORnet CDM, Sentinel CDM, CSV, and openEHR.

Run your first conversionChoose a conversionInstall

Project status

This documentation tracks the development version Convert-Pheno 0.34_1.

The established routes are used in research projects and covered by regression tests. Routes marked experimental have been tested with fewer independent datasets; their format guides state the current coverage.

Choose an interface

Start with the command-line interface. It supports files, mapping files, REDCap dictionaries, OMOP tables, terminology reports, and multi-entity BFF output.

From Convert-Pheno 0.35, the local Workbench provides a browser interface for supported JSON and file-based conversions. The API and module are intended for integration with other software.

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
• convert exported i2b2, PCORnet CDM, or Sentinel CDM tables to 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

Where to start

• 5-Minute Quickstart runs one small PXF-to-BFF conversion
• Choose a Conversion lists commands by input format
• Supported Formats summarizes accepted files and outputs
• Mapping Files explains project-specific CSV, REDCap, and ODM mappings
• Workbench covers the local browser interface available from version 0.35

Developer interfaces

• Module for local Perl or Python code
• API for HTTP(s) requests and the OpenAPI contract
• Implementation for the route registry and execution model
• Troubleshooting for common installation and input errors

External components

• GitHub repository