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ddomingof committed Jan 31, 2019
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Expand Up @@ -3,14 +3,16 @@ BioKEEN |build| |coverage| |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>`_.

Because we use PyKEEN as the underlying software package, implementations of 10 knowledge graph embedding models are currently
available for BioKEEN. Furthermore, BioKEEN can be run in *training mode* in which users provide their own set of hyper-parameter
values, or in *hyper-parameter optimization mode* to find suitable hyper-parameter values from set of user defined values.
Because we use PyKEEN as the underlying software package, implementations of 10 knowledge graph embedding models are
currently available for BioKEEN. Furthermore, BioKEEN can be run in *training mode* in which users provide their own set
of hyper-parameter values, or in *hyper-parameter optimization mode* to find suitable hyper-parameter values from set
of user defined values.

Through the integration of the `Bio2BEL <https://github.com/bio2bel>`_ software numerous biomedical databases are directly
accessible within BioKEEN.
Through the integration of the `Bio2BEL <https://github.com/bio2bel>`_ software numerous biomedical databases are
directly accessible within BioKEEN.

BioKEEN can also be run without having experience in programing by using its interactive command line interface that can be started with the command “biokeen” from a terminal.
BioKEEN can also be run without having experience in programing by using its interactive command line interface that can
be started with the command “biokeen” from a terminal.

Tutorial
--------
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