Convert Clinical Formats to BFF

Pheno-Ranker reads Beacon v2 Models (BFF) and Phenopackets v2 (PXF) directly. For other structured clinical standards, use Convert-Pheno to normalize the source data to BFF before comparison.

RoleConversion-assisted input

Clinical sourcesOMOP, openEHR, FHIR, REDCap, CDISC

Handoffindividuals.json (BFF)

ConfigurationBuilt in after conversion

Convert-Pheno performs source-aware clinical harmonization; Pheno-Ranker compares the resulting BFF individual records.

Why convert first?

Clinical standards encode identity, terminology, and repeated events differently. Convert-Pheno owns those source-specific mappings and groups the data into individual-level BFF records. Pheno-Ranker can then use its built-in BFF configuration and canonicalization instead of treating clinical JSON as an arbitrary structure.

Run This Format

First use Convert-Pheno to produce BFF individuals.json. Then run that BFF output in Pheno-Ranker; no source-format configuration is required.

Desktop

1. In Convert-Pheno, convert the clinical source to Beacon v2/BFF.
2. In Pheno-Ranker Desktop, select New analysis and choose cohort or patient mode.
3. Under User files, select the generated individuals.json as the reference.
4. In patient mode, also select a target record, then select Run analysis.

CLI

For cohort mode:

pheno-ranker -r individuals.json

For patient mode:

pheno-ranker -r individuals.json -t target.json

Continue with Cohort Mode, Patient Mode, or the full CLI Reference.

Source Format Guides

Use the maintained Convert-Pheno guide for your source format. These pages contain the current installation requirements, mapping scope, examples, and format-specific options.

Clinical source

OMOP-CDM

Consolidate relational clinical tables into individual-level BFF records.

Experimental mapping

openEHR

Group canonical compositions by patient and normalize their clinical content.

Experimental mapping

FHIR R4

Map supported Bundle resources into the corresponding BFF structures.

Clinical source

REDCap

Transform project exports into structured individual records.

Clinical research

CDISC-ODM

Normalize operational clinical-study data through the BFF target model.

Experimental mapping

CDISC Dataset-JSON

Convert supported tabular clinical-study datasets into BFF.

General-purpose data

This workflow is for clinical harmonization. To compare arbitrary categorical tables or custom records, use CSV Import or Generic JSON/YAML instead.

Review BFF inputContinue with cohort modeContinue with patient mode