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. 2021 May 1;37(4):586-587.
doi: 10.1093/bioinformatics/btaa718.

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database

Daniel Korn  1 , Tesia Bobrowski  2 , Michael Li  1 , Yaphet Kebede  3 , Patrick Wang  4 , Phillips Owen  3 , Gaurav Vaidya  3 , Eugene Muratov  2 , Rada Chirkova  5 , Chris Bizon  3 , Alexander Tropsha  2
Affiliations

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database

Daniel Korn et al. Bioinformatics. .

Abstract

Summary: In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP) biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to generate new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19 by establishing respective confirmatory pathways of drug action.

Availability and implementation: COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.

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Figures

Fig. 1.
Fig. 1.
Execution of a COVID-KOP query for linagliptin-COVID-19 pair. (A) Query graph; (B) answer graph for linagliptin-DPP4-T2D-COVID-19 pathway; (C) answer graph for linagliptin-ACE2-T2D-COVID-19 pathway
See this image and copyright information in PMC

Update of

References

    1. Ashburner M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25–29. - PMC - PubMed
    1. Barchetta I. et al. (2020) COVID-19 and diabetes: is this association driven by the DPP4 receptor? Potential clinical and therapeutic implications. Diabetes Res. Clin. Pract., 163, 108165. - PMC - PubMed
    1. Bizon C. et al. (2019) ROBOKOP KG and KGB: integrated knowledge graphs from federated sources. J. Chem. Inf. Model., 59, 4968–4973. - PMC - PubMed
    1. Fang L. et al. (2020) Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? Lancet Respir. Med., 8, e21. - PMC - PubMed
    1. Federhen S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136–D143. - PMC - PubMed

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