Supported formatsÂļ

%%{init: {'theme':'neutral'}}%% graph LR subgraph "Target Model" A[Beacon v2 Models] end A[Beacon v2 Models] -->|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; style A fill: #6495ED style A stroke: #6495ED style B fill: #FF7F50 style B stroke: #FF7F50 style C fill: #FF6965 style C stroke: #FF6965 style D fill: #3CB371 style D stroke: #3CB371 style E fill: #DDA0DD style E stroke: #DDA0DD style F fill: #FFFF00 style F stroke: #FFFF00
Convert-Pheno supported data conversions (May-21-2024)
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.

%%{init: {'theme':'neutral'}}%% graph LR A[Beacon v2 Models] -->|bff2jsonf| C[JSON Flattened]; A -->|bff2csv| D[CSV]; A -->|bff2jsonld| E[JSON-LD]; B[Phenopackets v2] -->|pxf2jsonf| C; B -->|pxf2csv| D; B -->|pxf2jsonld| E[JSON-LD]; 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
Convert-Pheno additional data conversions