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Faultless AST for Open Biomedical Ontologies.

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fastobo-py Star me

Faultless AST for Open Biomedical Ontologies in Python.

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


If your platform has no pre-built binaries available, you will need to have the Rust compiler installed. See the documentation on to learn how to install Rust on your machine.

Installation is then supported through pip:

$ pip install fastobo --user


An OboDoc instance can be instantiated from a file-handle or from a binary file handle using the fastobo.load function, or from a string using the fastobo.loads function.

import fastobo
obodoc = fastobo.load("../data/ms.obo")

Loading from a gzip file is supported:

import fastobo
import gzip
gzdoc = fastobo.load("../data/cl.obo.gz"))


Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker of the project if you need to report or ask something. If you are filling in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.


This project is currently being developed by Martin Larralde as part of a Master's Degree internship in the BBOP team of the Lawrence Berkeley National Laboratory, under the supervision of Chris Mungall.

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