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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

preprint
submitted on 25.11.2020, 22:21 and posted on 26.11.2020, 12:36 by Daniel Korn, Vera Pervitsky, Tesia Bobrowski, Vinicius Alves, Charles Schmitt, Cristopher Bizon, Nancy Baker, Rada Chirkova, Artem Cherkasov, Eugene Muratov, Alexander Tropsha

Objective: The COVID-19 pandemic has catalyzed a widespread effort to identify drug candidates and biological targets of relevance to SARS-COV-2 infection, which resulted in large numbers of publications on this subject. We have built the COVID-19 Knowledge Extractor (COKE), a web application to extract, curate, and annotate essential drug-target relationships from the research literature on COVID-19 to assist drug repurposing efforts.

Materials and Methods: SciBiteAI ontological tagging of the COVID Open Research Dataset (CORD-19), a repository of COVID-19 scientific publications, was employed to identify drug-target relationships. Entity identifiers were resolved through lookup routines using UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of protein and drug terms, and confidence scores were calculated for each entity pair.

Results: COKE processing of the current CORD-19 database identified about 3,000 drug-protein pairs, including 29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical trials for COVID-19.

Discussion: The rapidly evolving situation concerning the COVID-19 pandemic has resulted in a dramatic growth of publications on this subject in a short period. These circumstances call for methods that can condense the literature into the key concepts and relationships necessary for insights into SARS-CoV-2 drug repurposing.

Conclusion: The COKE repository and web application deliver key drug - target protein relationships to researchers studying SARS-CoV-2. COKE portal may provide comprehensive and critical information on studies concerning drug repurposing against COVID-19. COKE is freely available at https://coke.mml.unc.edu/ and the code is available at https://github.com/DnlRKorn/CoKE.

Funding

NCATS [OT2TR003441]

NIH [1U01CA207160]

History

Email Address of Submitting Author

murik@email.unc.edu

Institution

University of North Carolina

Country

United States

ORCID For Submitting Author

0000-0003-4616-7036

Declaration of Conflict of Interest

The authors declare no conflicts of interest.

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