Metadata-Version: 1.1
Name: ontobio
Version: 0.1.6
Summary: Library for working with OBO Library Ontologies and associations
Home-page: https://github.com/biolink/ontobio
Author: Chris Mungall
Author-email: cmungall@gmail.com
License: BSD
Description: |Build Status| |DOI|
        
        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 <https://www.pydoc.io/pypi/ontobio-0.1.6/index.html>`__ on
        pydoc.io
        
        Command Line
        ============
        
        See the README in the
        `bin <https://github.com/biolink/ontobio/tree/master/bin>`__ directory
        
        Notebooks
        =========
        
        See the `Jupyter
        Notebooks <http://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/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 <ontobio/ontol_manager.py>`__
        module. This creates an ontology object (see
        `ontol.py <ontobio/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 <https://github.com/geneontology/obographs>`__ spec.
        
        Associations
        ============
        
        See the ontobio.golr package
        
        .. |Build Status| image:: https://travis-ci.org/biolink/ontobio.svg?branch=master
           :target: https://travis-ci.org/biolink/ontobio
        .. |DOI| image:: https://zenodo.org/badge/13996/biolink/ontobio.svg
           :target: https://zenodo.org/badge/latestdoi/13996/biolink/ontobio
        
Keywords: ontology graph obo owl sparql networkx network
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Visualization
