5-Minute Quickstart

Convert one small Phenopacket into Beacon v2 Models (BFF). This route needs no mapping file or external terminology database.

1. Check the CLI

convert-pheno --version

If the command is unavailable, follow Download & Installation first.

2. Get the Example Input

Download the example Phenopacket and save it as phenopacket.json.

The file contains a one-record Phenopacket collection with one phenotypic feature. You can view the PXF format details later; they are not required for this example.

3. Run the Conversion

convert-pheno -ipxf phenopacket.json -obff individuals.json

The command creates individuals.json in the current directory. The result contains the individual patient-1, its normalized sex ontology term, and the HP:0001250 phenotypic feature.

You have completed a conversion

phenopacket.json was the source, -ipxf selected the input format, and -obff individuals.json selected the BFF output and filename.

4. Check the Result

Open individuals.json, or inspect its first lines:

head -40 individuals.json

For schema-aware checks, continue to Output Validation.

Where Next?

• Choose a Conversion for commands matching your own input and target formats.
• Supported Formats for the complete format overview.
• CLI Options & Behavior for output directories, multiple entities, ontology search, and large OMOP exports.
• Guided Examples for REDCap, OMOP-CDM, and mapped CSV walkthroughs.