Supported formats¶
Why start with these two?
Beacon v2 and Phenopackets v2 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 or encompass FHIR and other EHR data models
- Foster effective data sharing and integration initiatives
Note that these output formats are data exchange files that reach their full potential when loaded into a database. For instance, BFF can be loaded into a MongoDB database and their fields can be queried through an API, such as the Beacon v2 API.
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
.