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.
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
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.
- Mapping Files for an end-to-end REDCap mapping workflow.
- Regression fixtures for tested input and reference-output pairs across all implemented routes.