OpenBioLink

class OpenBioLink(create_inverse_triples=False, eager=False)

Bases: pykeen.datasets.base.PackedZipRemoteDataset

The OpenBioLink dataset.

OpenBioLink is an open-source, reproducible framework for generating biological knowledge graphs for benchmarking link prediction. It is available on GitHub at https://github.com/openbiolink/openbiolink and published in [breit2020]. There are four available datasets - this class represents the high quality, directed set.

breit2020

Breit, A. (2020) OpenBioLink: A benchmarking framework for large-scale biomedical link prediction, Bioinformatics

Initialize dataset.

Parameters

• url – The url where to download the dataset from

• name – The name of the file. If not given, tries to get the name from the end of the URL

• cache_root – An optional directory to store the extracted files. Is none is given, the default PyKEEN directory is used. This is defined either by the environment variable PYKEEN_HOME or defaults to ~/.pykeen.

• eager (bool) – Should the data be loaded eagerly? Defaults to false.

• create_inverse_triples (bool) – Should inverse triples be created? Defaults to false.