Supported Formats

This page gives a compact overview of the formats that Convert-Pheno can read and write. Internally, most conversions go through BFF first, and then continue to the requested output format when needed.

Beacon

BFF

Input and output. BFF output can include individuals, biosamples, datasets, and cohorts.

GA4GH

Phenopackets v2

Input and output for phenotypic and biosample-centered records.

Clinical DB

OMOP-CDM

SQL or CSV input, and CSV output for selected OMOP tables.

Mapping file

REDCap

CSV exports with data dictionary support and ontology search auditing.

Mapping file

CDISC-ODM

XML input using the same mapping model as other tabular conversions.

Mapping file

CSV

Generic tabular input for BFF, PXF, and OMOP output routes.

Note

openEHR support is currently experimental and currently limited to canonical composition input with BFF and PXF output. Patient identity must be resolvable from the payload or envelope, and multi-patient input is grouped automatically.

Supported conversions. Dotted blue lines go via BFF, which serves as the internal center model for most routes.

Input formats

• Beacon v2 Models (JSON | YAML)
• Phenopackets v2 (JSON | YAML)
• OMOP-CDM (SQL export | CSV)
• openEHR canonical JSON/YAML compositions (experimental)
• REDCap exports (CSV)
• CDISC-ODM v1 (XML)
• CSV raw data

Main output formats

• Beacon v2 Models (JSON | YAML)
• Phenopackets v2 (JSON | YAML)
• OMOP CDM (CSV)

Additional output formats

For BFF and PXF input, the tool can also produce simpler output forms that are easier to inspect or use downstream:

• flattened JSON or YAML with --ojsonf
• CSV with --ocsv
• JSON-LD or YAML-LD with --ojsonld

Additional output formats from BFF and PXF.

Why BFF matters in the diagrams

BFF is the internal center model for most conversions. User-facing output, however, is not limited to BFF: Convert-Pheno also supports PXF and OMOP CDM output paths.