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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.

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.

%%{init:{'theme':'neutral'}}%% graph LR subgraph "Target model" A[Beacon v2 Models] end A -->|bff2pxf| B[Phenopackets v2] C[REDCap] -->|redcap2pxf| B D[OMOP-CDM] -->|omop2bff| A E[CDISC-ODM] -->|cdisc2bff| A F[CSV] -->|csv2bff| A B -->|pxf2bff| A C -->|redcap2bff| A D -->|omop2pxf| B E -->|cdisc2pxf| B F -->|csv2pxf| B A -->|bff2omop| D F -->|csv2omop| D E -->|cdisc2omop| D C -->|redcap2omop| D B -->|pxf2omop| D style A fill:#6495ED,stroke:#6495ED style B fill:#FF7F50,stroke:#FF7F50 style C fill:#FF6965,stroke:#FF6965 style D fill:#3CB371,stroke:#3CB371 style E fill:#DDA0DD,stroke:#DDA0DD style F fill:#FFFF00,stroke:#FFFF00 linkStyle 1,7,8,9,11,12,13 stroke:#0000FF,stroke-width:1px,stroke-dasharray:5 5,opacity:0.5;
Supported conversions. Dotted blue lines go via BFF, which serves as the internal center model for most workflows.

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
%%{init: {'theme':'neutral'}}%% graph LR A[BFF] -->|bff2jsonf| C[JSON Flattened] A -->|bff2csv| D[CSV] A -->|bff2jsonld| E[JSON-LD] B[PXF] -->|pxf2jsonf| C B -->|pxf2csv| D B -->|pxf2jsonld| E style A fill:#6495ED,stroke:#6495ED style B fill:#FF7F50,stroke:#FF7F50 style C fill:#FFFF00,stroke:#FFFF00 style D fill:#E0E0E0,stroke:#E0E0E0 style E fill:#9999FF,stroke:#9999FF
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: the toolkit also supports PXF and OMOP CDM output paths.