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

doi:10.1093/bioinformatics/btaa718

. 2021 May 1;37(4):586-587.

doi: 10.1093/bioinformatics/btaa718.

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

Affiliations

¹ Department of Computer Science, University of North Carolina at Chapel Hill, USA.
² Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, USA.
³ Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7568, USA.
⁴ CoVar Applied Technologies, Durham, NC 27701, USA.
⁵ Department of Computer Science, North Carolina State University, Raleigh, NC 27606-5550, USA.

PMID: 33175089
PMCID: PMC7890668
DOI: 10.1093/bioinformatics/btaa718

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

Daniel Korn et al. Bioinformatics. 2021.

. 2021 May 1;37(4):586-587.

doi: 10.1093/bioinformatics/btaa718.

Authors

Affiliations

¹ Department of Computer Science, University of North Carolina at Chapel Hill, USA.
² Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, USA.
³ Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7568, USA.
⁴ CoVar Applied Technologies, Durham, NC 27701, USA.
⁵ Department of Computer Science, North Carolina State University, Raleigh, NC 27606-5550, USA.

PMID: 33175089
PMCID: PMC7890668
DOI: 10.1093/bioinformatics/btaa718

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.**
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

COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database.
Korn D, Bobrowski T, Li M, Kebede Y, Wang P, Owen P, Vaidya G, Muratov E, Chirkova R, Bizon C, Tropsha A. Korn D, et al. ChemRxiv [Preprint]. 2020 Jun 18. doi: 10.26434/chemrxiv.12462623. ChemRxiv. 2020. Update in: Bioinformatics. 2021 May 1;37(4):586-587. doi: 10.1093/bioinformatics/btaa718. PMID: 32601612 Free PMC article. Updated. Preprint.

Cited by

Synergistic and Antagonistic Drug Combinations against SARS-CoV-2.
Bobrowski T, Chen L, Eastman RT, Itkin Z, Shinn P, Chen CZ, Guo H, Zheng W, Michael S, Simeonov A, Hall MD, Zakharov AV, Muratov EN. Bobrowski T, et al. Mol Ther. 2021 Feb 3;29(2):873-885. doi: 10.1016/j.ymthe.2020.12.016. Epub 2020 Dec 15. Mol Ther. 2021. PMID: 33333292 Free PMC article.
[Overview of the application of knowledge graphs in the medical field].
Wang C, Zheng Z, Cai X, Huang J, Su Q. Wang C, et al. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2023 Oct 25;40(5):1040-1044. doi: 10.7507/1001-5515.202204016. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2023. PMID: 37879936 Free PMC article. Chinese.
Advances in the computational landscape for repurposed drugs against COVID-19.
Aronskyy I, Masoudi-Sobhanzadeh Y, Cappuccio A, Zaslavsky E. Aronskyy I, et al. Drug Discov Today. 2021 Dec;26(12):2800-2815. doi: 10.1016/j.drudis.2021.07.026. Epub 2021 Jul 30. Drug Discov Today. 2021. PMID: 34339864 Free PMC article. Review.
Discovery of Synergistic and Antagonistic Drug Combinations against SARS-CoV-2 In Vitro.
Bobrowski T, Chen L, Eastman RT, Itkin Z, Shinn P, Chen C, Guo H, Zheng W, Michael S, Simeonov A, Hall MD, Zakharov AV, Muratov EN. Bobrowski T, et al. bioRxiv [Preprint]. 2020 Jun 30:2020.06.29.178889. doi: 10.1101/2020.06.29.178889. bioRxiv. 2020. Update in: Mol Ther. 2021 Feb 3;29(2):873-885. doi: 10.1016/j.ymthe.2020.12.016. PMID: 32637956 Free PMC article. Updated. Preprint.
COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19.
Korn D, Pervitsky V, Bobrowski T, Alves VM, Schmitt C, Bizon C, Baker N, Chirkova R, Cherkasov A, Muratov E, Tropsha A. Korn D, et al. ChemRxiv [Preprint]. 2020 Nov 26. doi: 10.26434/chemrxiv.13289222. ChemRxiv. 2020. Update in: J Chem Inf Model. 2021 Dec 27;61(12):5734-5741. doi: 10.1021/acs.jcim.1c01285. PMID: 33269341 Free PMC article. Updated. Preprint.

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References

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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
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[1] Ashburner M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25–29. - PMC - PubMed

[2] Ashburner M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25–29. - PMC - PubMed

[3] 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

[4] 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

[5] Bizon C. et al. (2019) ROBOKOP KG and KGB: integrated knowledge graphs from federated sources. J. Chem. Inf. Model., 59, 4968–4973. - PMC - PubMed

[6] Bizon C. et al. (2019) ROBOKOP KG and KGB: integrated knowledge graphs from federated sources. J. Chem. Inf. Model., 59, 4968–4973. - PMC - PubMed

[7] 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

[8] 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

[9] Federhen S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136–D143. - PMC - PubMed

[10] Federhen S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136–D143. - PMC - PubMed

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

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

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