Molecular Systems Biology (Oct 2021)
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
- Marek Ostaszewski,
- Anna Niarakis,
- Alexander Mazein,
- Inna Kuperstein,
- Robert Phair,
- Aurelio Orta‐Resendiz,
- Vidisha Singh,
- Sara Sadat Aghamiri,
- Marcio Luis Acencio,
- Enrico Glaab,
- Andreas Ruepp,
- Gisela Fobo,
- Corinna Montrone,
- Barbara Brauner,
- Goar Frishman,
- Luis Cristóbal Monraz Gómez,
- Julia Somers,
- Matti Hoch,
- Shailendra Kumar Gupta,
- Julia Scheel,
- Hanna Borlinghaus,
- Tobias Czauderna,
- Falk Schreiber,
- Arnau Montagud,
- Miguel Ponce de Leon,
- Akira Funahashi,
- Yusuke Hiki,
- Noriko Hiroi,
- Takahiro G Yamada,
- Andreas Dräger,
- Alina Renz,
- Muhammad Naveez,
- Zsolt Bocskei,
- Francesco Messina,
- Daniela Börnigen,
- Liam Fergusson,
- Marta Conti,
- Marius Rameil,
- Vanessa Nakonecnij,
- Jakob Vanhoefer,
- Leonard Schmiester,
- Muying Wang,
- Emily E Ackerman,
- Jason E Shoemaker,
- Jeremy Zucker,
- Kristie Oxford,
- Jeremy Teuton,
- Ebru Kocakaya,
- Gökçe Yağmur Summak,
- Kristina Hanspers,
- Martina Kutmon,
- Susan Coort,
- Lars Eijssen,
- Friederike Ehrhart,
- Devasahayam Arokia Balaya Rex,
- Denise Slenter,
- Marvin Martens,
- Nhung Pham,
- Robin Haw,
- Bijay Jassal,
- Lisa Matthews,
- Marija Orlic‐Milacic,
- Andrea Senff-Ribeiro,
- Karen Rothfels,
- Veronica Shamovsky,
- Ralf Stephan,
- Cristoffer Sevilla,
- Thawfeek Varusai,
- Jean‐Marie Ravel,
- Rupsha Fraser,
- Vera Ortseifen,
- Silvia Marchesi,
- Piotr Gawron,
- Ewa Smula,
- Laurent Heirendt,
- Venkata Satagopam,
- Guanming Wu,
- Anders Riutta,
- Martin Golebiewski,
- Stuart Owen,
- Carole Goble,
- Xiaoming Hu,
- Rupert W Overall,
- Dieter Maier,
- Angela Bauch,
- Benjamin M Gyori,
- John A Bachman,
- Carlos Vega,
- Valentin Grouès,
- Miguel Vazquez,
- Pablo Porras,
- Luana Licata,
- Marta Iannuccelli,
- Francesca Sacco,
- Anastasia Nesterova,
- Anton Yuryev,
- Anita de Waard,
- Denes Turei,
- Augustin Luna,
- Ozgun Babur,
- Sylvain Soliman,
- Alberto Valdeolivas,
- Marina Esteban‐Medina,
- Maria Peña‐Chilet,
- Kinza Rian,
- Tomáš Helikar,
- Bhanwar Lal Puniya,
- Dezso Modos,
- Agatha Treveil,
- Marton Olbei,
- Bertrand De Meulder,
- Stephane Ballereau,
- Aurélien Dugourd,
- Aurélien Naldi,
- Vincent Noël,
- Laurence Calzone,
- Chris Sander,
- Emek Demir,
- Tamas Korcsmaros,
- Tom C Freeman,
- Franck Augé,
- Jacques S Beckmann,
- Jan Hasenauer,
- Olaf Wolkenhauer,
- Egon L Willighagen,
- Alexander R Pico,
- Chris T Evelo,
- Marc E Gillespie,
- Lincoln D Stein,
- Henning Hermjakob,
- Peter D'Eustachio,
- Julio Saez‐Rodriguez,
- Joaquin Dopazo,
- Alfonso Valencia,
- Hiroaki Kitano,
- Emmanuel Barillot,
- Charles Auffray,
- Rudi Balling,
- Reinhard Schneider,
- the COVID‐19 Disease Map Community
Affiliations
- Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Anna Niarakis
- Université Paris‐Saclay Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ Genhotel Univ Evry Evry France
- Alexander Mazein
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Inna Kuperstein
- Institut Curie PSL Research University Paris France
- Robert Phair
- Integrative Bioinformatics, Inc. Mountain View CA USA
- Aurelio Orta‐Resendiz
- Institut Pasteur Université de Paris, Unité HIV Inflammation et Persistance Paris France
- Vidisha Singh
- Université Paris‐Saclay Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ Genhotel Univ Evry Evry France
- Sara Sadat Aghamiri
- Inserm‐ Institut national de la santé et de la recherche médicale Paris France
- Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Andreas Ruepp
- Institute of Experimental Genetics (IEG) Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH) Neuherberg Germany
- Gisela Fobo
- Institute of Experimental Genetics (IEG) Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH) Neuherberg Germany
- Corinna Montrone
- Institute of Experimental Genetics (IEG) Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH) Neuherberg Germany
- Barbara Brauner
- Institute of Experimental Genetics (IEG) Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH) Neuherberg Germany
- Goar Frishman
- Institute of Experimental Genetics (IEG) Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH) Neuherberg Germany
- Luis Cristóbal Monraz Gómez
- Institut Curie PSL Research University Paris France
- Julia Somers
- Department of Molecular and Medical Genetics Oregon Health & Sciences University Portland OR USA
- Matti Hoch
- Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany
- Shailendra Kumar Gupta
- Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany
- Julia Scheel
- Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany
- Hanna Borlinghaus
- Department of Computer and Information Science University of Konstanz Konstanz Germany
- Tobias Czauderna
- Faculty of Information Technology Department of Human‐Centred Computing Monash University Clayton Vic. Australia
- Falk Schreiber
- Department of Computer and Information Science University of Konstanz Konstanz Germany
- Arnau Montagud
- Barcelona Supercomputing Center (BSC) Barcelona Spain
- Miguel Ponce de Leon
- Barcelona Supercomputing Center (BSC) Barcelona Spain
- Akira Funahashi
- Department of Biosciences and Informatics Keio University Yokohama Japan
- Yusuke Hiki
- Department of Biosciences and Informatics Keio University Yokohama Japan
- Noriko Hiroi
- Graduate School of Media and Governance Keio Research Institute at SFC Keio University Kanagawa Japan#
- Takahiro G Yamada
- Department of Biosciences and Informatics Keio University Yokohama Japan
- Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial‐Resistant Pathogens Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany
- Alina Renz
- Computational Systems Biology of Infections and Antimicrobial‐Resistant Pathogens Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany
- Muhammad Naveez
- Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany
- Zsolt Bocskei
- Sanofi R&D Translational Sciences Chilly‐Mazarin France
- Francesco Messina
- Dipartimento di Epidemiologia Ricerca Pre‐Clinica e Diagnostica Avanzata National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S. Rome Italy
- Daniela Börnigen
- Bioinformatics Core Facility Universitätsklinikum Hamburg‐Eppendorf Hamburg Germany
- Liam Fergusson
- Royal (Dick) School of Veterinary Medicine The University of Edinburgh Edinburgh UK
- Marta Conti
- Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany
- Marius Rameil
- Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany
- Vanessa Nakonecnij
- Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany
- Jakob Vanhoefer
- Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany
- Leonard Schmiester
- Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany
- Muying Wang
- Department of Chemical and Petroleum Engineering University of Pittsburgh Pittsburgh PA USA
- Emily E Ackerman
- Department of Chemical and Petroleum Engineering University of Pittsburgh Pittsburgh PA USA
- Jason E Shoemaker
- Department of Chemical and Petroleum Engineering University of Pittsburgh Pittsburgh PA USA
- Jeremy Zucker
- Pacific Northwest National Laboratory Richland WA USA
- Kristie Oxford
- Pacific Northwest National Laboratory Richland WA USA
- Jeremy Teuton
- Pacific Northwest National Laboratory Richland WA USA
- Ebru Kocakaya
- Stem Cell Institute Ankara University Ankara Turkey
- Gökçe Yağmur Summak
- Stem Cell Institute Ankara University Ankara Turkey
- Kristina Hanspers
- Institute of Data Science and Biotechnology Gladstone Institutes San Francisco CA USA
- Martina Kutmon
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Susan Coort
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Lars Eijssen
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Friederike Ehrhart
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine Yenepoya (Deemed to be University) Mangalore India
- Denise Slenter
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Marvin Martens
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Nhung Pham
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Robin Haw
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Bijay Jassal
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Lisa Matthews
- NYU Grossman School of Medicine New York NY USA
- Marija Orlic‐Milacic
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Andrea Senff-Ribeiro
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Karen Rothfels
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Veronica Shamovsky
- NYU Grossman School of Medicine New York NY USA
- Ralf Stephan
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Cristoffer Sevilla
- European Bioinformatics Institute (EMBL‐EBI) European Molecular Biology Laboratory Hinxton, Cambridgeshire UK
- Thawfeek Varusai
- European Bioinformatics Institute (EMBL‐EBI) European Molecular Biology Laboratory Hinxton, Cambridgeshire UK
- Jean‐Marie Ravel
- INSERM UMR_S 1256 Nutrition, Genetics, and Environmental Risk Exposure (NGERE) Faculty of Medicine of Nancy University of Lorraine Nancy France
- Rupsha Fraser
- Queen's Medical Research Institute The University of Edinburgh Edinburgh UK
- Vera Ortseifen
- Senior Research Group in Genome Research of Industrial Microorganisms Center for Biotechnology Bielefeld University Bielefeld Germany
- Silvia Marchesi
- Department of Surgical Science Uppsala University Uppsala Sweden
- Piotr Gawron
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Ewa Smula
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Laurent Heirendt
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology Oregon Health & Science University Portland OR USA
- Anders Riutta
- Institute of Data Science and Biotechnology Gladstone Institutes San Francisco CA USA
- Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Stuart Owen
- Department of Computer Science The University of Manchester Manchester UK
- Carole Goble
- Department of Computer Science The University of Manchester Manchester UK
- Xiaoming Hu
- Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden Dresden Germany
- Dieter Maier
- Biomax Informatics AG Planegg Germany
- Angela Bauch
- Biomax Informatics AG Planegg Germany
- Benjamin M Gyori
- Harvard Medical School Laboratory of Systems Pharmacology Boston MA USA
- John A Bachman
- Harvard Medical School Laboratory of Systems Pharmacology Boston MA USA
- Carlos Vega
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Valentin Grouès
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Miguel Vazquez
- Barcelona Supercomputing Center (BSC) Barcelona Spain
- Pablo Porras
- European Bioinformatics Institute (EMBL‐EBI) European Molecular Biology Laboratory Hinxton, Cambridgeshire UK
- Luana Licata
- Department of Biology University of Rome Tor Vergata Rome Italy
- Marta Iannuccelli
- Department of Biology University of Rome Tor Vergata Rome Italy
- Francesca Sacco
- Department of Biology University of Rome Tor Vergata Rome Italy
- Anastasia Nesterova
- Elsevier Philadelphia PA USA
- Anton Yuryev
- Elsevier Philadelphia PA USA
- Anita de Waard
- Research Collaborations Unit Elsevier Jericho VT USA
- Denes Turei
- Institute for Computational Biomedicine Heidelberg University Heidelberg Germany
- Augustin Luna
- cBio Center, Divisions of Biostatistics and Computational Biology Department of Data Sciences Dana‐Farber Cancer Institute Boston MA USA
- Ozgun Babur
- Computer Science Department University of Massachusetts Boston Boston MA USA
- Sylvain Soliman
- Lifeware Group Inria Saclay‐Ile de France Palaiseau France
- Alberto Valdeolivas
- Institute for Computational Biomedicine Heidelberg University Heidelberg Germany
- Marina Esteban‐Medina
- Clinical Bioinformatics Area Fundación Progreso y Salud (FPS) Hospital Virgen del Rocio Sevilla Spain
- Maria Peña‐Chilet
- Clinical Bioinformatics Area Fundación Progreso y Salud (FPS) Hospital Virgen del Rocio Sevilla Spain
- Kinza Rian
- Clinical Bioinformatics Area Fundación Progreso y Salud (FPS) Hospital Virgen del Rocio Sevilla Spain
- Tomáš Helikar
- Department of Biochemistry University of Nebraska‐Lincoln Lincoln NE USA
- Bhanwar Lal Puniya
- Department of Biochemistry University of Nebraska‐Lincoln Lincoln NE USA
- Dezso Modos
- Quadram Institute Bioscience Norwich UK
- Agatha Treveil
- Quadram Institute Bioscience Norwich UK
- Marton Olbei
- Quadram Institute Bioscience Norwich UK
- Bertrand De Meulder
- European Institute for Systems Biology and Medicine (EISBM) Vourles France
- Stephane Ballereau
- Cancer Research UK Cambridge Institute University of Cambridge Cambridge UK
- Aurélien Dugourd
- Institute for Computational Biomedicine Heidelberg University Heidelberg Germany
- Aurélien Naldi
- Lifeware Group Inria Saclay‐Ile de France Palaiseau France
- Vincent Noël
- Institut Curie PSL Research University Paris France
- Laurence Calzone
- Institut Curie PSL Research University Paris France
- Chris Sander
- cBio Center, Divisions of Biostatistics and Computational Biology Department of Data Sciences Dana‐Farber Cancer Institute Boston MA USA
- Emek Demir
- Department of Molecular and Medical Genetics Oregon Health & Sciences University Portland OR USA
- Tamas Korcsmaros
- Quadram Institute Bioscience Norwich UK
- Tom C Freeman
- The Roslin Institute University of Edinburgh Edinburgh UK
- Franck Augé
- Sanofi R&D Translational Sciences Chilly‐Mazarin France
- Jacques S Beckmann
- University of Lausanne Lausanne Switzerland
- Jan Hasenauer
- Helmholtz Zentrum München – German Research Center for Environmental Health Institute of Computational Biology Neuherberg Germany
- Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany
- Egon L Willighagen
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Alexander R Pico
- Institute of Data Science and Biotechnology Gladstone Institutes San Francisco CA USA
- Chris T Evelo
- Department of Bioinformatics ‐ BiGCaT NUTRIM Maastricht University Maastricht The Netherlands
- Marc E Gillespie
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Lincoln D Stein
- MaRS Centre Ontario Institute for Cancer Research Toronto ON Canada
- Henning Hermjakob
- European Bioinformatics Institute (EMBL‐EBI) European Molecular Biology Laboratory Hinxton, Cambridgeshire UK
- Peter D'Eustachio
- NYU Grossman School of Medicine New York NY USA
- Julio Saez‐Rodriguez
- Institute for Computational Biomedicine Heidelberg University Heidelberg Germany
- Joaquin Dopazo
- Clinical Bioinformatics Area Fundación Progreso y Salud (FPS) Hospital Virgen del Rocio Sevilla Spain
- Alfonso Valencia
- Barcelona Supercomputing Center (BSC) Barcelona Spain
- Hiroaki Kitano
- Systems Biology Institute Tokyo Japan
- Emmanuel Barillot
- Institut Curie PSL Research University Paris France
- Charles Auffray
- European Institute for Systems Biology and Medicine (EISBM) Vourles France
- Rudi Balling
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- the COVID‐19 Disease Map Community
- DOI
- https://doi.org/10.15252/msb.202110387
- Journal volume & issue
-
Vol. 17,
no. 10
pp. n/a – n/a
Abstract
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.
Keywords
- computable knowledge repository
- large‐scale biocuration
- omics data analysis
- open access community effort
- systems biomedicine