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BioKEEN (KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings

Project description

BioKEEN (Biological KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings built on PyKEEN.

Installation Current version on PyPI Stable Supported Python Versions MIT License

  1. BioKEEN can be installed with the following commands:

python3 -m pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git@master
  1. or in editable mode with:

$ 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:

biokeen

or alternatively:

python3 -m biokeen

Starting BioKEEN’s training/HPO pipeline

To configure an experiment, please run following command:

biokeen start

or alternatively:

python3 -m biokeen start

To start BioKEEN with an existing configuration file, please run the following command:

biokeen start -c /path/to/config.json

or alternatively:

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:

biokeen predict -m /path/to/model/directory -d /path/to/data/directory

or alternatively:

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 repository, run:

biokeen get <name>

Where <name> can be any repository name in Bio2BEL such as hippie, mirtarbase.

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