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A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
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KG-Hub-building and exchanging biological knowledge graphs.

J Harry Caufield1, Tim Putman2, Kevin Schaper2

  • 1Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.

Bioinformatics (Oxford, England)
|June 30, 2023
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Summary
This summary is machine-generated.

KG-Hub provides a standardized platform for building and sharing biological knowledge graphs (KGs). This facilitates data integration and reuse across diverse research areas, including disease research and drug discovery.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Science

Background:

  • Knowledge graphs (KGs) are crucial for integrating diverse biological data and enabling inference.
  • A lack of standardized solutions hinders the construction, exchange, and downstream application of biological KGs.

Purpose of the Study:

  • To introduce KG-Hub, a novel platform for the standardized creation, sharing, and utilization of biological KGs.
  • To address the limitations in current KG development and promote broader data integration and reuse.

Main Methods:

  • Developed KG-Hub with a modular extract-transform-load (ETL) pattern for Biolink Model compliance.
  • Integrated Open Biological and Biomedical Ontologies (OBO) and cloud storage for KG artifacts.
  • Implemented versioning, automated updates, and stable URLs for KG builds.

Main Results:

  • KG-Hub supports standardized KG construction, exchange, and reuse.
  • The platform facilitates integration with graph machine learning (ML) tools for automated analysis.
  • Current projects demonstrate KG-Hub's utility in COVID-19 research, drug repurposing, and rare disease studies.

Conclusions:

  • KG-Hub offers a comprehensive solution for managing biological knowledge graphs.
  • The platform enhances data accessibility and promotes advanced analytics, including ML applications.
  • KG-Hub is available at https://kghub.org.