Metadata-Version: 2.1
Name: wc-onto
Version: 0.0.2
Summary: Ontology for whole-cell modeling
Home-page: https://github.com/KarrLab/wc_onto
Author: Karr Lab
Author-email: info@karrlab.org
License: MIT
Download-URL: https://github.com/KarrLab/wc_onto
Keywords: whole-cell modeling single cell computational systems biology dynamical modeling bioinformatics ontology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: configobj
Requires-Dist: pronto (>=1)
Requires-Dist: requests
Requires-Dist: setuptools
Requires-Dist: wc-utils
Provides-Extra: all
Requires-Dist: mock ; extra == 'all'
Requires-Dist: sphinx (>=1.8) ; extra == 'all'
Requires-Dist: sphinx-fontawesome ; extra == 'all'
Requires-Dist: sphinx-rtd-theme (>=0.4.2) ; extra == 'all'
Requires-Dist: sphinxcontrib-addmetahtml (>=0.1.1) ; extra == 'all'
Requires-Dist: sphinxcontrib-bibtex ; extra == 'all'
Requires-Dist: sphinxcontrib-googleanalytics (>=0.1.1) ; extra == 'all'
Requires-Dist: sphinxcontrib-spelling ; extra == 'all'
Requires-Dist: sphinxprettysearchresults ; extra == 'all'
Provides-Extra: docs
Requires-Dist: sphinx (>=1.8) ; extra == 'docs'
Requires-Dist: sphinx-fontawesome ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme (>=0.4.2) ; extra == 'docs'
Requires-Dist: sphinxcontrib-addmetahtml (>=0.1.1) ; extra == 'docs'
Requires-Dist: sphinxcontrib-bibtex ; extra == 'docs'
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Requires-Dist: sphinxcontrib-spelling ; extra == 'docs'
Requires-Dist: sphinxprettysearchresults ; extra == 'docs'
Provides-Extra: tests
Requires-Dist: mock ; extra == 'tests'

|Documentation| |Test results| |Test coverage| |Code analysis| |License|
|Analytics|

WC-Onto
=======

Ontology for whole-cell modeling

Installation
------------

Installing the ontology for use in Python
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Install this Python package with pip

   ::

       pip install git+https://github.com/KarrLab/wc_onto.git#egg=wc_onto[all]

   This command will install this Python package, including the ontology
   (in OBO format) and the Python code for using the ontology. Once
   installed, the ontology will be located at
   ``pkg_resources.resource_filename('wc_onto', 'onto.obo')``.

2. Obtain a `BioPortal API key <http://bioportal.bioontology.org/>`__
3. Save your BioPortal API key to a configuration file
   (``~/.wc/wc_onto.cfg``)

   ::

       [wc_onto]
           [[bioportal]]
               key = <BioPortal API key>

4. Import the package. The other ontologies which wc\_onto references
   will automatically be downloaded the first time that the package is
   imported.

   ::

       from wc_onto import onto

Downloading the ontology
~~~~~~~~~~~~~~~~~~~~~~~~

Alternatively, the ontology can be downloaded (in OBO format) from
GitHub or BioPortal

-  Download `latest
   revision <https://raw.githubusercontent.com/KarrLab/wc_onto/master/wc_onto/onto.obo>`__
   from GitHub
-  Download `latest
   snapshot <https://bioportal.bioontology.org/ontologies/WC>`__ from
   BioPortal

Documentation
-------------

Please see the `API documentation <https://docs.karrlab.org/wc_onto>`__.

License
-------

The package is released under the `MIT license <LICENSE>`__.

Development team
----------------

This package was developed by the `Karr Lab <https://www.karrlab.org>`__
at the Icahn School of Medicine at Mount Sinai in New York, USA.

Questions and comments
----------------------

Please contact the `Karr Lab <https://www.karrlab.org>`__ with any
questions or comments.

.. |Documentation| image:: https://readthedocs.org/projects/wc-onto/badge/?version=latest
   :target: https://docs.karrlab.org/wc_onto
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   :target: https://coveralls.io/github/KarrLab/wc_onto
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   :target: https://codeclimate.com/github/KarrLab/wc_onto
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   :target: LICENSE
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