Library for working with OBO Library Ontologies and associations

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  • License: BSD License (BSD)
  • Author: Chris Mungall
  • Tags ontology, graph, obo, owl, sparql, networkx, network
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ontobio - a python API for working with ontologies and associations

This module provides objects and utility methods for working with ontologies and associations of entities (genes, variants, etc) to ontology classes.

The ontologies and associations can either be local files or provided by remote services (currently the OntoBee SPARQL service for ontologies and a Monarch or GO Golr service for associations).

API Docs

ontobio on pydoc.io

Command Line

See the README in the bin directory

Notebooks

See the Jupyter Notebooks for code examples

Basics

There are two ways of initiating an ontology object:

  • via a local obo-json file

  • via remote connections to OBO PURLs

  • via remote query to a SPARQL service (currently ontobee, but soon others)

Persistent caching is used (currently cachier) to avoid repeated expensive I/O connections

This is handled via the ontol_manager.py module. This creates an ontology object (see ontol.py ).

Note that object modeling is lightweight - we use the python networkx package for representing the basic graph portion of an ontology. See also the obographs spec.

Associations

See the ontobio.golr package

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Avatar for cmungall from gravatar.com cmungall Avatar for deepakunni3 from gravatar.com deepakunni3 Avatar for dustine32 from gravatar.com dustine32 Avatar for kltm from gravatar.com kltm Avatar for mugitty from gravatar.com mugitty Avatar for smoxon from gravatar.com smoxon

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: BSD License (BSD)
  • Author: Chris Mungall
  • Tags ontology, graph, obo, owl, sparql, networkx, network
Classifiers

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2.9.10

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