A software toolkit for the interconversion of standard data models for phenotypic data
[](https://github.com/cnag-biomedical-informatics/convert-pheno/actions/workflows/build-and-test.yml) [](https://coveralls.io/github/CNAG-Biomedical-Informatics/convert-pheno?branch=main) [](https://github.com/cnag-biomedical-informatics/convert-pheno/actions/workflows/cpan-publish.yml)  [](https://github.com/cnag-biomedical-informatics/convert-pheno/actions/workflows/docker-build-multi-arch.yml) [](https://hub.docker.com/r/manuelrueda/convert-pheno/) [](https://github.com/cnag-biomedical-informatics/convert-pheno/actions/workflows/documentation.yml) [](https://opensource.org/licenses/Artistic-2.0) --- [๐ Documentation](https://cnag-biomedical-informatics.github.io/convert-pheno) ยท [๐ป Installation](https://cnag-biomedical-informatics.github.io/convert-pheno/download-and-installation) ยท [๐ Google Colab](https://colab.research.google.com/drive/1T6F3bLwfZyiYKD6fl1CIxs9vG068RHQ6?usp=sharing) ยท [๐ฆ CPAN](https://metacpan.org/pod/Convert::Pheno) ยท [๐ณ Docker](https://hub.docker.com/r/manuelrueda/convert-pheno/tags) # Convert-Pheno `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 native desktop application. ## Quick Start ```bash 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-db ``` Entity-aware BFF output can write individuals, biosamples, datasets, and cohorts when the selected source route supports them: ```bash convert-pheno -ipxf phenopacket.json \ -obff --entities individuals biosamples datasets cohorts \ --out-dir bff_out/ ``` See the [command-line interface guide](https://cnag-biomedical-informatics.github.io/convert-pheno/use-as-a-command-line-interface) for commands by source and target, or run `convert-pheno --help` for the full CLI option list. ## Installation - [Non-containerized installation](non-containerized/README.md) - [Docker installation](docker/README.md) ## Desktop Application From Convert-Pheno 0.35, a native desktop application provides route selection, local file handling, conversion runs, output previews, and terminology review. See the [desktop application guide](https://cnag-biomedical-informatics.github.io/convert-pheno/graphical-interface). ## Tested Examples Synthetic fixtures under [`t/`](t/README.md) provide tested inputs and reference outputs for the supported conversion routes. ## Citation Rueda, M et al. (2024). *Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data*. Journal of Biomedical Informatics.