krassowski / obonet

OBO-formatted ontologies → networkx (Python 3)

obonet: load OBO-formatted ontologies into networkx

Read OBO-formatted ontologies in Python. obonet is

• user friendly
• no nonsense
• pythonic
• modern
• simple and tested
• lightweight
• networkx leveraging

This Python 3.4+ package loads OBO serialized ontologies into networks. The function obonet.read_obo() takes an .obo file and returns a networkx.MultiDiGraph representation of the ontology. The parser was designed for the OBO specification version 1.2 & 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/obonet/raw/master/tests/data/taxrank.obo'
graph = obonet.read_obo(url)

# Or read the xz-compressed taxrank ontology
url = 'https://github.com/dhimmel/obonet/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')

For a more detailed tutorial, see the Gene Ontology example notebook.

Installation

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

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