Metadata-Version: 2.1
Name: biokeen
Version: 0.0.4
Summary: BioKEEN (KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings
Home-page: https://github.com/SmartDataAnalytics/BioKEEN
Author: Mehdi Ali
Author-email: mehdi.ali@cs.uni-bonn.de
Maintainer: Mehdi Ali
Maintainer-email: mehdi.ali@cs.uni-bonn.de
License: MIT
Description: BioKEEN |build| |docs| |zenodo|
        ===============================
        
        BioKEEN (Biological KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings built on
        `PyKEEN <https://github.com/SmartDataAnalytics/PyKEEN>`_.
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        1. ``BioKEEN`` can be installed with the following commands:
        
        .. code-block:: sh
        
            python3 -m pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git@master
        
        2. or in editable mode with:
        
        .. code-block:: sh
        
            $ git clone https://github.com/SmartDataAnalytics/BioKEEN.git biokeen
            $ cd biokeen
            $ python3 -m pip install -e .
        
        How to Use
        ----------
        To show BioKEEN's available commands, please run following command:
        
        .. code-block:: sh
        
            biokeen
        
        or alternatively:
        
        .. code-block:: python
        
            python3 -m biokeen
        
        
        Starting BioKEEN's training/HPO pipeline
        ****************************************
        To configure an experiment, please run following command:
        
        .. code-block:: sh
        
            biokeen start
        
        or alternatively:
        
        .. code-block:: python
        
            python3 -m biokeen start
        
        
        To start BioKEEN with an existing configuration file, please run the following command:
        
        .. code-block:: sh
        
            biokeen start -c /path/to/config.json
        
        or alternatively:
        
        .. code-block:: python
        
            python3 -m biokeen start -c /path/to/config.json
        
        
        Starting BioKEEN's prediction pipeline
        **************************************
        To make prediction based on a trained model, please run following command:
        
        .. code-block:: sh
        
            biokeen predict -m /path/to/model/directory -d /path/to/data/directory
        
        or alternatively:
        
        .. code-block:: python
        
            python3 -m biokeen predict -m /path/to/model/directory -d /path/to/data/directory
        
        
        Getting Bio2BEL Data
        ********************
        To download and structure the data from a `Bio2BEL <https://github.com/bio2bel>`_ repository, run:
        
        .. code-block:: python
        
            biokeen get <name>
        
        Where ``<name>`` can be any repository name in Bio2BEL such as ``hippie``, ``mirtarbase``.
        
        .. |build| image:: https://travis-ci.org/SmartDataAnalytics/BioKEEN.svg?branch=master
            :target: https://travis-ci.org/SmartDataAnalytics/BioKEEN
        .. |zenodo| image:: https://zenodo.org/badge/150270965.svg
           :target: https://zenodo.org/badge/latestdoi/150270965
        .. |docs| image:: http://readthedocs.org/projects/biokeen/badge/?version=latest
            :target: https://biokeen.readthedocs.io/en/latest/
            :alt: Documentation Status
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/biokeen.svg
            :alt: Stable Supported Python Versions
        .. |pypi_version| image:: https://img.shields.io/pypi/v/biokeen.svg
            :alt: Current version on PyPI
        .. |pypi_license| image:: https://img.shields.io/pypi/l/biokeen.svg
            :alt: MIT License
        
        
Keywords: KEEN,knowledge embedding
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6
Provides-Extra: docs
