COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
Marek Ostaszewski(University of Luxembourg), Anna Niarakis(Université Paris-Saclay), Alexander Mazein(University of Luxembourg), Inna Kuperstein(Inserm), Robert D. Phair, Aurelio Orta‐Resendiz(Institut Pasteur), Vidisha Singh(Université Paris-Saclay), Sara Sadat Aghamiri(Inserm), Márcio Luís Acencio(University of Luxembourg), Enrico Glaab(University of Luxembourg), Andreas Ruepp(Helmholtz Zentrum München), Gisela Fobo(Helmholtz Zentrum München), Corinna Montrone(Helmholtz Zentrum München), Barbara Brauner(Helmholtz Zentrum München), Goar Frishman(Helmholtz Zentrum München), Luis Cristóbal Monraz Gómez(Inserm), Julia Somers(Oregon Health & Science University), Matti Hoch(University of Rostock), Shailendra K. Gupta(University of Rostock), Julia Scheel(University of Rostock), Hanna Borlinghaus(University of Konstanz), Tobias Czauderna(Monash University), Falk Schreiber(University of Konstanz), Arnau Montagud(Barcelona Supercomputing Center), Miguel Ponce-de-León(Barcelona Supercomputing Center), Akira Funahashi(Keio University), Yusuke Hiki(Keio University), Noriko Hiroi(Keio University Shonan Fujisawa), Takahiro Yamada(Keio University), Andreas Dräger(German Center for Infection Research), Alina Renz(University of Tübingen), Muhammad Naveez(Riga Technical University), Zsolt Böcskei(Sanofi (France)), Francesco Messina(Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani), Daniela Börnigen(Universität Hamburg), Liam Fergusson(Royal College of Physicians of Edinburgh), Marta Zaffira Conti(University of Bonn), Marius Rameil(University of Bonn), Vanessa Nakonecnij(University of Bonn), Jakob Vanhoefer(University of Bonn), Leonard Schmiester(University of Bonn), Muying Wang(University of Pittsburgh), Emily E. Ackerman(University of Pittsburgh), Jason E. Shoemaker(University of Pittsburgh), Jeremy Zucker(Pacific Northwest National Laboratory), Kristie Oxford(Pacific Northwest National Laboratory), Jeremy Teuton(Pacific Northwest National Laboratory), Ebru Kocakaya(Ankara University), Gökçe Yağmur Summak(Ankara University), Kristina Hanspers(Gladstone Institutes), Martina Kutmon(Maastricht University), Susan L. Coort(Maastricht University), Lars Eijssen(Maastricht University Medical Centre), Friederike Ehrhart(Maastricht University Medical Centre), Rex Devasahayam Arokia Balaya(Yenepoya University), Denise Slenter(Maastricht University), Marvin Martens(Maastricht University), Nhung Pham(Maastricht University), Robin Haw(Ontario Institute for Cancer Research), Bijay Jassal(Ontario Institute for Cancer Research), Lisa Matthews(New York University), M Orlic-Milacic(Ontario Institute for Cancer Research), Andrea Senff‐Ribeiro(Ontario Institute for Cancer Research), Karen Rothfels(Ontario Institute for Cancer Research), Veronica Shamovsky(New York University), Ralf Stephan(Ontario Institute for Cancer Research), Cristoffer Sevilla(European Bioinformatics Institute), Thawfeek Varusai(European Bioinformatics Institute), Jean‐Marie Ravel(Inserm), Rupsha Fraser(The Queen's Medical Research Institute), Vera Ortseifen(Bielefeld University), Silvia Marchesi(Uppsala University), Piotr Gawron(University of Luxembourg), Ewa Smula(University of Luxembourg), Laurent Heirendt(University of Luxembourg), Venkata Satagopam(University of Luxembourg), Guanming Wu(Oregon Health & Science University), Anders Riutta(Gladstone Institutes), Martin Golebiewski(Heidelberg Institute for Theoretical Studies), Stuart Owen(University of Manchester), Carole Goble(University of Manchester), Xiaoming Hu(Heidelberg Institute for Theoretical Studies), Rupert W. Overall(German Center for Neurodegenerative Diseases), Dieter Maier(Biomax Informatics (Germany)), Angela Bauch(Biomax Informatics (Germany)), Benjamin M. Gyori(Harvard University), John A. Bachman(Harvard University), Carlos Vega(University of Luxembourg), Valentin Grouès(University of Luxembourg), Miguél Vázquez(Barcelona Supercomputing Center), Pablo Porras(European Bioinformatics Institute), Luana Licata(University of Rome Tor Vergata), Marta Iannuccelli(University of Rome Tor Vergata), Francesca Sacco(University of Rome Tor Vergata), Anastasia Nesterova(RELX Group (United States)), Anton Yuryev(RELX Group (United States)), Anita de Waard(RELX Group (Netherlands)), Dénes Türei(Heidelberg University), Augustin Luna(Harvard University), Özgün Babur(University of Massachusetts Boston), Sylvain Soliman(Centre Inria de Saclay), Alberto Valdeolivas(Heidelberg University), Marina Esteban‐Medina(Fundación Progreso y Salud), María Peña-Chilet(Fundación Progreso y Salud), Kinza Rian(Fundación Progreso y Salud), Tomáš Helikar(University of Nebraska–Lincoln), Bhanwar Lal Puniya(University of Nebraska–Lincoln), Dezső Módos(Quadram Institute), Agatha Treveil(Quadram Institute), Márton Ölbei(Quadram Institute), Bertrand De Meulder(European Institute for Systems Biology and Medicine), Stéphane Ballereau(University of Cambridge), Aurélien Dugourd(Heidelberg University), Aurélien Naldi(Centre Inria de Saclay), Vincent Noël(Inserm), Laurence Calzone(Inserm), Chris Sander(Harvard University), Emek Demir(Oregon Health & Science University), Tamás Korcsmáros(Quadram Institute), Tom C. Freeman(Roslin Institute), Franck Augé(Sanofi (France)), J. Beckmann(University of Lausanne), Jan Hasenauer(University of Bonn), Olaf Wolkenhauer(University of Rostock), Egon Willighagen(Maastricht University), Alexander R. Pico(Gladstone Institutes), Chris T. Evelo(Maastricht University), Marc Gillespie(Ontario Institute for Cancer Research), Lincoln Stein(Ontario Institute for Cancer Research), Henning Hermjakob(European Bioinformatics Institute), Peter D’Eustachio(New York University), Julio Sáez-Rodríguez(Heidelberg University), Joaquı́n Dopazo(Fundación Progreso y Salud), Alfonso Valencia(Institució Catalana de Recerca i Estudis Avançats), Hiroaki Kitano(Okinawa Institute of Science and Technology Graduate University), Emmanuel Barillot(Inserm), Charles Auffray(University of Cambridge), Rudi Balling(University of Luxembourg), Reinhard Schneider(University of Luxembourg), the COVID‐19 Disease Map Community
Cited by 110Open Access
Abstract
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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