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OpenBioLink — pykeen 1.11.2-dev documentation

Getting Started

• Installation
• First Steps
• Knowledge Graph Embedding Models
• Representations
• Interaction Functions
• Tracking Results during Training
• Saving Checkpoints during Training
• A Toy Example with Translational Distance Models
• Understanding the Evaluation
• Optimizing a Model’s Hyper-parameters
• Running an Ablation Study
• Performance Tricks
• Getting Started with NodePiece
• Inductive Link Prediction
• Splitting
• PyTorch Lightning Integration
• Using Resolvers
• Normalizer, Constrainer & Regularizer
• Troubleshooting

Bring Your Own

• Bring Your Own Data
• Bring Your Own Interaction

Extending PyKEEN

• Extending the Datasets
• Extending the Models

Reference

• Pipeline
• Models
• Datasets
  • pykeen.datasets Package
    • Functions
    • Classes
      • Dataset
      • AristoV4
      • Hetionet
      • Kinships
      • Nations
      • OpenBioLink
      • OpenBioLinkLQ
      • CoDExSmall
      • CoDExMedium
      • CoDExLarge
      • CN3l
      • OGBBioKG
      • OGBWikiKG2
      • UMLS
      • FB15k
      • FB15k237
      • WK3l15k
      • WK3l120k
      • WN18
      • WN18RR
      • YAGO310
      • DRKG
      • BioKG
      • ConceptNet
      • CKG
      • CSKG
      • DBpedia50
      • DB100K
      • OpenEA
      • Countries
      • WD50KT
      • Wikidata5M
      • PharmKG8k
      • PharmKG
      • PrimeKG
      • Globi
      • PharMeBINet
    • Variables
    • Class Inheritance Diagram
  • pykeen.datasets.base Module
  • pykeen.datasets.analysis Module
• Inductive Datasets
• Entity Alignment
• Triples
• Triples Workflows
• Training
• Stoppers
• Loss Functions
• Loss Weighting
• Regularizers
• Result Trackers
• Negative Sampling
• Filtering
• Optimizers
• Evaluation
• Metrics
• Hyper-parameter Optimization
• Ablation
• Prediction
• Uncertainty
• Sealant
• Constants
• Flexible Weight Checkpoints
• pykeen.nn
• Utilities

Appendix

• Analysis
• References

• Datasets
• OpenBioLink
• View page source

class OpenBioLink(**kwargs)[source]

Bases: 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.

Initialize the OpenBioLink dataset.

Parameters:

kwargs – keyword arguments passed to pykeen.datasets.base.PackedZipRemoteDataset.

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