KG-COVID-19: Knowledge Graph for COVID-19 Response

The goal of the KG-COVID-19 project is to use Machine Learning (ML) to generate useful COVID-related knowledge. Rich biological knowledge exists about SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), for example genomics, epidemiology, susceptibility, clinical/symptoms, viral lifecycle, pathways, and inhibitors. However, much of this information is either locked in textual form in the literature, or in individual siloed databases, making integrative prediction difficult and costly.

To address this challenge, we have produced we have produced a COVID-19 knowledge graph (KG) to support both DOE and international COVID-19 efforts: https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki

This knowledge graph incorporates up-to-date data extracted from biomedical databases and literature, including drug, protein-protein interactions, SARS-CoV-2 gene annotations, concept and publication data from the CORD19 data set. We also ingest the Human Phenotype Ontology, the Gene Ontology, and Mondo for phenotype, gene annotations and diseases, respectively, in order to integrate the data in an ontology-aware way.

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We are currently applying machine learning (ML) techniques to discover new links (for example, identifying existing drugs that could be repurposed to treat COVID-19) and generate actionable knowledge. In addition, we are providing this knowledge graph to the COVID-19 research community in order to accelerate COVID-19 research.

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People:

  • Justin Reese - LBNL
  • Deepak Unni - LBNL
  • Marcin Joachimiak - LBNL
  • Chris Mungall - LBNL

External Collaborators:

  • Peter Robinson - Jackson Laboratory
  • Tiffany Callahan - University of Colorado Denver
  • Luca Cappelletti - University of Milan
  • Vida Ravanmehr - Jackson Laboratory
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