Welcome to BioPAX2Cadbiom’s documentation!

Biopax2cabiom is a script to transform BioPAX RDF data from a triplestore to a CADBIOM model.

Contents:

• Installation
  • Using Docker
  • From sources for developers
• Usage
  • Named Arguments
  • Sub-commands:
• Documentation of the package for developers
  • biopax_converter
  • cadbiom_writer
  • classes
  • sparql_biopaxQueries
  • namespaces
  • sparql_wrapper
• Documentation of tests for developers
  • Cases
  • Queries
  • Functions
• Tutorial
  • How to make queries on an endpoint like Pathway Commons?
  • Generated files
• Examples
  • Examples of conversions from BioPAX graphs towards Cadbiom models
• Troubleshooting
  • Verbose and debug output
  • Conversion issues
• Contribute

Indices and tables

• Index
• Module Index
• Search Page