Metadata-Version: 2.1
Name: pybel_ols
Version: 0.0.1
Summary: A package for building BEL resource files with the EBI Ontology Lookup Service.
Home-page: https://github.com/pybel/pybel-ols
Author: Charles Tapley Hoyt
Author-email: charles.hoyt@scai.fraunhofer.de
Maintainer: Charles Tapley Hoyt
Maintainer-email: charles.hoyt@scai.fraunhofer.de
License: MIT License
Download-URL: https://github.com/pybel/pybel-ols/releases
Project-URL: Bug Tracker, https://github.com/pybel/pybel-ols/issues
Project-URL: Source Code, https://github.com/pybel/pybel-ols
Description: PyBEL-OLS |build| |coverage| |documentation|
        ============================================
        A PyBEL [1]_ extension for building BEL resources with the EBI [2]_ Ontology
        Lookup Service.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        Get the Latest
        ~~~~~~~~~~~~~~~
        Download the most recent code from `GitHub <https://github.com/pybel/pybel-ols>`_ with:
        
        .. code-block:: sh
        
           $ pip install git+https://github.com/pybel/pybel-ols.git
        
        For Developers
        ~~~~~~~~~~~~~~
        Clone the repository from `GitHub <https://github.com/pybel/pybel-ols>`_ and install in editable mode with:
        
        .. code-block:: sh
        
           $ git clone https://github.com/pybel/pybel-ols.git
           $ cd pybel-ols
           $ pip install -e .
        
        Getting Started
        ---------------
        The main goal is to generate a namespace file. For example, to generate a namespace for the `Human Phenotype Ontology
        <https://www.ebi.ac.uk/ols/ontologies/hp>`_, abbreviated with the prefix ``hp``, the following command can be used:
        
        .. code-block:: sh
        
           $ pybel-ols namespace_from_ols hp --encoding "O" --output ~/Desktop/hp.belns
        
        Where ``--encoding "O"`` tells it that all terms in this ontology correspond to the pathology/phenotype BEL type.
        
        Alternatively, the '-b' option can be used to specify an alternate OLS instance
        
        .. code-block:: bash
        
            $ pybel-ols namespace_from_ols hp --encoding O --output ~/Desktop/hp.belns -b https://localhost/ols
        
        References
        ----------
        .. [1] Hoyt, C. T., *et al.* (2017). `PyBEL: a Computational Framework for Biological Expression Language
               <https://doi.org/10.1093/bioinformatics/btx660>`_. Bioinformatics, 34(December), 1–2.
        
        .. [2] Cote, R., *et al.* (2006). `The Ontology Lookup Service, a lightweight cross-platform tool for controlled
               vocabulary queries <https://doi.org/10.1186/1471-2105-7-97>`_. BMC Bioinformatics, 7, 1–7.
        
        .. |build| image:: https://travis-ci.org/pybel/pybel-ols.svg?branch=master
            :target: https://travis-ci.org/pybel/pybel-ols
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/pybel/pybel-ols/coverage.svg?branch=master
            :target: https://codecov.io/gh/pybel/pybel-ols?branch=master
            :alt: Coverage Status
        
        .. |documentation| image:: https://readthedocs.org/projects/pybel-ols/badge/?version=latest
            :target: https://pybel.readthedocs.io/projects/ols/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/pybel-ols.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/pybel-ols.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/pybel-ols.svg
            :alt: MIT License
        
Keywords: Biological Expression Language,BEL,Semantic Web,Networks Biology,Systems Biology,Ontologies
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6
Provides-Extra: docs
