# -*- coding: utf-8 -*-
"""The OpenBioLink dataset.
Get a summary with ``python -m pykeen.datasets.openbiolink``
"""
import logging
import click
from .base import PackedZipRemoteDataSet
__all__ = [
'OpenBioLink',
'OpenBioLinkF1',
'OpenBioLinkF2',
'OpenBioLinkLQ',
]
HQ_URL = 'https://samwald.info/res/OpenBioLink_2020_final/HQ_DIR.zip'
F1_URL = 'https://github.com/PyKEEN/pykeen-openbiolink-benchmark/raw/master/filter_1/openbiolink_f1.zip'
F2_URL = 'https://github.com/PyKEEN/pykeen-openbiolink-benchmark/raw/master/filter_2/openbiolink_f2.zip'
LQ_URL = 'https://samwald.info/res/OpenBioLink_2020_final/ALL_DIR.zip'
[docs]class OpenBioLink(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 <https://doi.org/10.1093/bioinformatics/btaa274>`_, *Bioinformatics*
"""
def __init__(self, create_inverse_triples: bool = False, eager: bool = False):
super().__init__(
url=HQ_URL,
name='HQ_DIR.zip',
relative_training_path='HQ_DIR/train_test_data/train_sample.csv',
relative_testing_path='HQ_DIR/train_test_data/test_sample.csv',
relative_validation_path='HQ_DIR/train_test_data/val_sample.csv',
eager=eager,
create_inverse_triples=create_inverse_triples,
)
[docs]class OpenBioLinkF1(PackedZipRemoteDataSet):
"""The PyKEEN First Filtered OpenBioLink 2020 Dataset."""
def __init__(self, create_inverse_triples: bool = False, eager: bool = False):
super().__init__(
url=F1_URL,
name='openbiolink_f1.zip',
relative_training_path='train.tsv',
relative_testing_path='test.tsv',
relative_validation_path='val.tsv',
eager=eager,
create_inverse_triples=create_inverse_triples,
)
[docs]class OpenBioLinkF2(PackedZipRemoteDataSet):
"""The PyKEEN Second Filtered OpenBioLink 2020 Dataset."""
def __init__(self, create_inverse_triples: bool = False, eager: bool = False):
super().__init__(
url=F2_URL,
name='openbiolink_f2.zip',
relative_training_path='train.tsv',
relative_testing_path='test.tsv',
relative_validation_path='val.tsv',
eager=eager,
create_inverse_triples=create_inverse_triples,
)
[docs]class OpenBioLinkLQ(PackedZipRemoteDataSet):
"""The low-quality variant of the OpenBioLink dataset."""
def __init__(self, create_inverse_triples: bool = False, eager: bool = False):
super().__init__(
url=LQ_URL,
name='ALL_DIR.zip',
relative_training_path='ALL_DIR/train_test_data/train_sample.csv',
relative_testing_path='ALL_DIR/train_test_data/test_sample.csv',
relative_validation_path='ALL_DIR/train_test_data/val_sample.csv',
eager=eager,
create_inverse_triples=create_inverse_triples,
)
@click.command()
def _main():
ds = OpenBioLink()
click.echo(ds.summary_str())
if __name__ == '__main__':
logging.basicConfig(level=logging.INFO)
_main()