Supported formats¶
%%{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
%% dotted, thinner, semi‑transparent blue for the “must via BFF” shortcuts
linkStyle 1,7,8,9,11,12,13 stroke:#0000FF,stroke-width:1px,stroke-dasharray:5 5,opacity:0.5;
Note: Dotted blue lines → must go via Beacon v2 Models
Main¶
Why GA4GH Beacon v2 and Phenopackets v2?
Beacon v2 [BFF] and Phenopackets v2 [PXF] are data exchange standards from the GA4GH. They:
- Allow for storing both phenotypic and genomic data, a key component in today's research
- Facilitate streamlined data representation in genomic and biomedical research environments
- Play a central role in mapping exercises due to their structured and compact data schemas
- Are not intended to replace other health data
- Foster effective data sharing and integration initiatives
Additional Output Formats¶
Given that Beacon v2 Models and Phenopackets v2 utilize JSON to encode data in a complex tree-like structure, this format presents challenges for straightforward analytics. To mitigate this and enhance data usability, we provide options to convert from BFF/PXF to more analytics-friendly formats:
- "Flattened" (a.k.a., folded) JSON or YAML with the option
--ojsonf - CSV with the option
--ocsv
Additionally, we are working on a conversion to JSON-LD, a format that is compatible with the RDF ecosystem, used in many healthcare-related data systems.
- 🧪 JSON-LD (or YAML-LD) with the option
--jsonld
Hint
Note that you can convert from any accepted input format to either BFF or PXF.
%%{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
style A stroke: #6495ED
style B fill: #FF7F50
style B stroke: #FF7F50
style C fill: #FFFF00
style C stroke: #FFFF00
style D fill: #EOEOEO
style D stroke: #EOEOEO
style E fill: #9999FF
style E stroke: #9999FF