A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
Abstract MotivationIn the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, hostpathogen and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy. ResultsHere, we describe a workflow we designed for a semi-automated integration of rapidly emerging datasets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 74,805 host-host protein and 1,265 drug-target interactions. The resultant Neo4j graph database named “Neo4COVID19” is accessible via a web interface and via API calls based on the Bolt protocol. We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19. Availabilityhttps://neo4covid19.ncats.io
Zahor¨￠nszky-K?halmi Gergely、Siramshetty Vishal B.、Math¨| Ewy A.、Hall Matthew D.、Michael Samuel G.、Mestres Jordi、Jensen Lars J.、Mierzwa Tim、Gurumurthy Manideep、Kumar Praveen、Godfrey Alexander G.、Grillo Busola、Simon Reid、Oprea Tudor I.、Mathew Biju、Metaxatos Dimitrios、Grishagin Ivan、Backus Mark、Brovold Laura
National Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesResearch Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu FabraNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesDepartment of Internal Medicine, University of New Mexico School of Medicine||Department of Computer Science, University of New MexicoNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesDepartment of Internal Medicine, University of New Mexico School of Medicine||Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen||UNM Comprehensive Cancer Center||Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of GothenburgNational Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesNational Center for Advancing Translational Sciences||Rancho BioSciences LLCNational Center for Advancing Translational SciencesRancho BioSciences LLC
医学研究方法生物科学研究方法、生物科学研究技术药学
SARS-CoV-2COVID-19network pharmacologygraph databaseNeo4jdata integrationdrug repositioning
Zahor¨￠nszky-K?halmi Gergely,Siramshetty Vishal B.,Math¨| Ewy A.,Hall Matthew D.,Michael Samuel G.,Mestres Jordi,Jensen Lars J.,Mierzwa Tim,Gurumurthy Manideep,Kumar Praveen,Godfrey Alexander G.,Grillo Busola,Simon Reid,Oprea Tudor I.,Mathew Biju,Metaxatos Dimitrios,Grishagin Ivan,Backus Mark,Brovold Laura.A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research[EB/OL].(2025-03-28)[2025-05-17].https://www.biorxiv.org/content/10.1101/2020.11.04.369041.点此复制
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