{ "info": { "author": "Charles Tapley Hoyt", "author_email": "charles.hoyt@scai.fraunhofer.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 1 - Planning", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3 :: Only" ], "description": "PyBEL-OLS |build| |coverage| |documentation|\n============================================\nA PyBEL [1]_ extension for building BEL resources with the EBI [2]_ Ontology\nLookup Service.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\nGet the Latest\n~~~~~~~~~~~~~~~\nDownload the most recent code from `GitHub `_ with:\n\n.. code-block:: sh\n\n $ pip install git+https://github.com/pybel/pybel-ols.git\n\nFor Developers\n~~~~~~~~~~~~~~\nClone the repository from `GitHub `_ and install in editable mode with:\n\n.. code-block:: sh\n\n $ git clone https://github.com/pybel/pybel-ols.git\n $ cd pybel-ols\n $ pip install -e .\n\nGetting Started\n---------------\nThe main goal is to generate a namespace file. For example, to generate a namespace for the `Human Phenotype Ontology\n`_, abbreviated with the prefix ``hp``, the following command can be used:\n\n.. code-block:: sh\n\n $ pybel-ols namespace_from_ols hp --encoding \"O\" --output ~/Desktop/hp.belns\n\nWhere ``--encoding \"O\"`` tells it that all terms in this ontology correspond to the pathology/phenotype BEL type.\n\nAlternatively, the '-b' option can be used to specify an alternate OLS instance\n\n.. code-block:: bash\n\n $ pybel-ols namespace_from_ols hp --encoding O --output ~/Desktop/hp.belns -b https://localhost/ols\n\nReferences\n----------\n.. [1] Hoyt, C. T., *et al.* (2017). `PyBEL: a Computational Framework for Biological Expression Language\n `_. Bioinformatics, 34(December), 1\u20132.\n\n.. [2] Cote, R., *et al.* (2006). `The Ontology Lookup Service, a lightweight cross-platform tool for controlled\n vocabulary queries `_. BMC Bioinformatics, 7, 1\u20137.\n\n.. |build| image:: https://travis-ci.org/pybel/pybel-ols.svg?branch=master\n :target: https://travis-ci.org/pybel/pybel-ols\n :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/pybel/pybel-ols/coverage.svg?branch=master\n :target: https://codecov.io/gh/pybel/pybel-ols?branch=master\n :alt: Coverage Status\n\n.. |documentation| image:: https://readthedocs.org/projects/pybel-ols/badge/?version=latest\n :target: https://pybel.readthedocs.io/projects/ols/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pybel-ols.svg\n :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/pybel-ols.svg\n :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/pybel-ols.svg\n :alt: MIT License\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "https://github.com/pybel/pybel-ols/releases", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/pybel/pybel-ols", "keywords": "Biological Expression Language,BEL,Semantic Web,Networks Biology,Systems Biology,Ontologies", "license": "MIT License", "maintainer": "Charles Tapley Hoyt", "maintainer_email": "charles.hoyt@scai.fraunhofer.de", "name": "pybel-ols", "package_url": "https://pypi.org/project/pybel-ols/", "platform": "", "project_url": "https://pypi.org/project/pybel-ols/", "project_urls": { "Bug Tracker": "https://github.com/pybel/pybel-ols/issues", "Download": "https://github.com/pybel/pybel-ols/releases", "Homepage": "https://github.com/pybel/pybel-ols", "Source Code": "https://github.com/pybel/pybel-ols" }, "release_url": "https://pypi.org/project/pybel-ols/0.0.1/", "requires_dist": [ "pybel", "bel-resources (>=0.0.2)", "click", "ols-client", "sphinx ; extra == 'docs'", "sphinx-rtd-theme ; extra == 'docs'", "sphinx-click ; extra == 'docs'", "sphinx-autodoc-typehints ; extra == 'docs'" ], "requires_python": ">=3.6", "summary": "A package for building BEL resource files with the EBI Ontology Lookup Service.", "version": "0.0.1" }, "last_serial": 4760152, "releases": { "0.0.1": [ { "comment_text": "", "digests": { "md5": "486cfbc248dd125d81bf3600b1a54b66", "sha256": "c95eea119fd575f190931bf3167425bc2498622533e289b0ac7e1b2b108eb01c" }, "downloads": -1, "filename": "pybel_ols-0.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "486cfbc248dd125d81bf3600b1a54b66", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 8213, "upload_time": "2019-01-30T15:13:55", "url": "https://files.pythonhosted.org/packages/ab/be/8b90e81433468f8aa149b499a4afb8bbbe5d13dc9b538eb086f42e9ebfed/pybel_ols-0.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "8e6535ee3622a4d37684b7b0a833bb79", "sha256": "609a6861bcf2cc22debaf109574432f0a8ae91f6f0c03361d4fbf6cff0792763" }, "downloads": -1, "filename": "pybel_ols-0.0.1.tar.gz", "has_sig": false, "md5_digest": "8e6535ee3622a4d37684b7b0a833bb79", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 10375, "upload_time": "2019-01-30T15:13:57", "url": "https://files.pythonhosted.org/packages/9a/0a/c07b533bdb6a7055b65de5d1cf712c3ca18d623d336ed742103925bd3d48/pybel_ols-0.0.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "486cfbc248dd125d81bf3600b1a54b66", "sha256": "c95eea119fd575f190931bf3167425bc2498622533e289b0ac7e1b2b108eb01c" }, "downloads": -1, "filename": "pybel_ols-0.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "486cfbc248dd125d81bf3600b1a54b66", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 8213, "upload_time": "2019-01-30T15:13:55", "url": "https://files.pythonhosted.org/packages/ab/be/8b90e81433468f8aa149b499a4afb8bbbe5d13dc9b538eb086f42e9ebfed/pybel_ols-0.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "8e6535ee3622a4d37684b7b0a833bb79", "sha256": "609a6861bcf2cc22debaf109574432f0a8ae91f6f0c03361d4fbf6cff0792763" }, "downloads": -1, "filename": "pybel_ols-0.0.1.tar.gz", "has_sig": false, "md5_digest": "8e6535ee3622a4d37684b7b0a833bb79", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 10375, "upload_time": "2019-01-30T15:13:57", "url": "https://files.pythonhosted.org/packages/9a/0a/c07b533bdb6a7055b65de5d1cf712c3ca18d623d336ed742103925bd3d48/pybel_ols-0.0.1.tar.gz" } ] }