Choose an Input Format

Choose the shortest path

Pheno-Ranker reads BFF and PXF directly. Convert other clinical standards to BFF with Convert-Pheno. For non-clinical categorical data, use the generic JSON/YAML or CSV workflows.

GA4GH native

BFF

Beacon v2 individuals.json; no custom configuration required.

GA4GH native

PXF

Phenopackets v2 records; no custom configuration required.

Clinical harmonization

Convert to BFF

Prepare OMOP, openEHR, FHIR, REDCap, or CDISC data with Convert-Pheno.

Beyond GA4GH

CSV

Converted to JSON plus configuration with csv2pheno-ranker.

Beyond GA4GH

Generic JSON/YAML

Custom categorical records described by a configuration file.

Clinical standards

For OMOP-CDM, openEHR, FHIR R4, REDCap, and CDISC data, use Convert-Pheno to produce BFF individuals.json, then run Pheno-Ranker with its built-in BFF handling.

YAML / JSON

Use this path for an array of categorical JSON or YAML records that does not follow BFF or PXF. A small configuration identifies the record ID and the fields to compare. Nested arrays are handled automatically. Follow the MoviePackets tutorial for a complete example.

CSV

We developed a utility that converts CSV files to JSON and automatically creates the configuration file needed. See an example on how to use it here.