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.
%%{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;
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
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.