A software toolkit for the interconversion of standard data models for phenotypic data
📘 Documentation · 💻 Installation · 📓 Google Colab · 📦 CPAN · 🐳 Docker
Convert-Pheno converts clinical and phenotypic records between BFF,
Phenopackets (PXF), OMOP-CDM, REDCap, CSV, CDISC formats, FHIR R4, openEHR,
cBioPortal, i2b2, PCORnet CDM, and Sentinel CDM.
The command-line interface is the primary interface. The same conversion engine is also available through a Perl module, Python binding, HTTP(s) API, and local graphical Workbench.
convert-pheno -ipxf phenopacket.json -obff individuals.json
convert-pheno -ibff individuals.json -opxf phenopackets.json
convert-pheno -iomop omop-export/ -obff individuals.json --ohdsi-dbEntity-aware BFF output can write individuals, biosamples, datasets, and cohorts when the selected source route supports them:
convert-pheno -ipxf phenopacket.json \
-obff --entities individuals biosamples datasets cohorts \
--out-dir bff_out/See Choose a Conversion
for commands by source and target, or run convert-pheno --help for the full
CLI option list.
From Convert-Pheno 0.35, the Docker image includes a local graphical interface for supported JSON and file-based routes:
docker run --rm \
--publish 127.0.0.1:8080:8080 \
manuelrueda/convert-pheno:latestOpen http://127.0.0.1:8080. The Workbench is intended for local use and has a 100 MiB request limit. Use the CLI for streaming or larger inputs.
Synthetic fixtures under t/ provide tested inputs and reference
outputs for the supported conversion routes.
Rueda, M et al. (2024). Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data. Journal of Biomedical Informatics. https://doi.org/10.1016/j.jbi.2023.104558
Manuel Rueda, PhD. CNAG: https://www.cnag.eu