OpenBioLink¶

class OpenBioLink(create_inverse_triples=False, eager=False)[source]¶

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 data sets - 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.