fastobo

Faultless AST for Open Biomedical Ontologies in Python.

About

fastobo is a Rust library implementing a reliable parser for the OBO file format 1.4. This extension module exports idiomatic Python bindings that can be used to load, edit and serialize ontologies in the OBO format.

Setup

Run pip install fastobo in a shell to download the latest release from PyPi, or have a look at the Installation page to find other ways to install diced.

Library

• User Guide
  • Installation
  • Publications
  • Changelog
• Examples
  • Checking empty descriptions
  • Looking for obsolete terms without replacements
  • Loading an OBO ontology into a networkx graph
• API Reference
  • Functions
  • Data structures
  • Exceptions

License

This library is provided under the MIT license.

This project was was developed by Martin Larralde during his MSc thesis at the Lawrence Berkeley National Laboratory in the BBOP team.