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A python parser for OBO ontology files

Build Status

This repository contains a python package for handling OBO serialized ontologies. The function obonet.read_obo() takes an .obo file and returns a networkx.MultiDiGraph representation of the ontology.

The parser aims to be compatible with OBO versions 1.2 and 1.4.

Usage

This package is designed and tested on python ≥ 3.4. OBO files can be read from a path, URL, or open file handle. Compression is inferred from the path's extension. See example usage below:

import networkx
import obonet

# Read the taxrank ontology
url = 'https://github.com/dhimmel/obo/raw/master/tests/data/taxrank.obo'
graph = obonet.read_obo(url)

# Or read the xz-compressed taxrank ontology
url = 'https://github.com/dhimmel/obo/raw/master/tests/data/taxrank.obo.xz'
graph = obonet.read_obo(url)

# Number of nodes
len(graph)

# Number of edges
graph.number_of_edges()

# Check if the ontology is a DAG
networkx.is_directed_acyclic_graph(graph)

# Mapping from term ID to name
id_to_name = {id_: data['name'] for id_, data in graph.nodes(data=True)}
id_to_name['TAXRANK:0000006']  # TAXRANK:0000006 is species

# Find all superterms of species. Note that networkx.descendants gets
# superterms, while networkx.ancestors returns subterms.
networkx.descendants(graph, 'TAXRANK:0000006')

Installation

PyPI

The recommended approach is to install the latest release from PyPI using:

pip install obonet

However, if you'd like to install the most recent version from GitHub, use:

pip install git+https://github.com/dhimmel/obonet.git#egg=obonet

Contributing

GitHub issues

We welcome feature suggestions and community contributions. Currently, only reading OBO files is supported. Please open an issue if you're interested in writing OBO files in Python.

Release instructions

This section is only relevant for project maintainers. Travis CI deployments are used to upload releases to PyPI. To create a new release, do the following:

  1. Bump the __version__ in obonet/__init__.py.

  2. Run the following commands:

TAG=v`python setup.py --version`
git add obonet/__init__.py
git commit --message="Upgrade to $TAG"
git push
git tag --annotate $TAG --message="Upgrade to $TAG"
git push --tags