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COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 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; 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 Drager; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Daniela Bornigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie L Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Rex D. A. B.; 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 Mohamed Varusai; Jean-Marie Ravel; 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 Overall; Dieter Maier; Angela Bauch; Benjamin M Gyori; John A Bachman; Carlos Vega; Valentin Groues; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Pena-Chilet; Kinza Rian; Tomas Helikar; Bhanwar Lal Puniya; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Dezso Modos; Agatha Treveil; Marton Laszlo Olbei; Bertrand De Meulder; Aurelien Naldi; Aurelien Dugourd; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Auge; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon Willighagen; Alexander R Pico; Chris Evelo; Lincoln D Stein; Henning Hermjakob; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; - the COVID-19 Disease Map Community.
Afiliação
  • Marek Ostaszewski; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
  • Anna Niarakis; Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, 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., 346 Paul Ave, Mountain View, CA, USA
  • Aurelio Orta-Resendiz; Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France
  • Vidisha Singh; Laboratoire Europeen de Recherche pour la Polyarthrite Rhumatoide - Genhotel, Univ Evry, Universite Paris-Saclay, 2, rue Gaston Cremieux, 91057 EVRY-GENOPOLE ce
  • Sara Sadat Aghamiri; Inserm- Institut national de la sante et de la recherche medicale. Saint-Louis Hospital 1 avenue Claude Vellefaux Pavillon Bazin 75475 Paris
  • 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 Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764
  • Gisela Fobo; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764
  • Corinna Montrone; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764
  • Barbara Brauner; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764
  • Goar Frishman; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764
  • Julia Somers; Oregong Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239
  • Matti Hoch; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
  • Shailendra Kumar Gupta; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
  • Julia Scheel; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
  • Hanna Borlinghaus; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
  • Tobias Czauderna; Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, 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; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
  • Yusuke Hiki; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
  • Noriko Hiroi; Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884
  • Takahiro G Yamada; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522
  • Andreas Drager; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu
  • Alina Renz; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu
  • Muhammad Naveez; Riga Technical University, Institute of Applied Computer Systems,1 Kalku Street, LV-1658 Riga, Latvia
  • Zsolt Bocskei; Sanofi R&D Translational Sciences
  • Daniela Bornigen; Bioinformatics Core Facility, Universitaetsklinikum Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
  • Liam Fergusson; The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG
  • Marta Conti; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
  • Marius Rameil; University of 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; Helmholtz Zentrum Munchen - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany
  • Muying Wang; Department of Chemical Engineering, University of Pittsburgh
  • Emily E Ackerman; University of Pittsburgh, Department of Chemical and Petroleum Engineering
  • Jason E Shoemaker; Dept. of Chemical & Petroleum Engineering, University of Pittsburgh
  • Jeremy Zucker; Pacific Northwest National Laboratory
  • Kristie L Oxford; Pacific Northwest National Laboratory
  • Jeremy Teuton; Pacific Northwest National Laboratory
  • Ebru Kocakaya; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY
  • Gokce Yagmur Summak; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY
  • Kristina Hanspers; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158
  • Martina Kutmon; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
  • Susan Coort; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands
  • Lars Eijssen; Department of Bioninformatics-BiGCaT, NUTRIM, Maastricht University, Universiteitssingel 60, 6229 ER Maastricht, The Netherlands
  • Friederike Ehrhart; Maastricht University, Department of Bioinformatics, NUTRIM, Universiteitssingel 60; 6229 ER Maastricht; The Netherlands
  • Rex D. A. B.; Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
  • Denise Slenter; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
  • Marvin Martens; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands
  • Nhung Pham; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands
  • Robin Haw; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
  • Bijay Jassal; Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada
  • Lisa Matthews; NYU Grossman School of Medicine, New York NY 10016 USA
  • Marija Orlic-Milacic; Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada
  • Andrea Senff-Ribeiro; Ontario Institute for Cancer Research (OICR) (Canada)
  • Karen Rothfels; Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada
  • Veronica Shamovsky; NYU Langone Medical Center, New York, USA
  • Ralf Stephan; Ontario Institute for Cancer Research, MaRS Centre, 661 University Ave, Suite 510, Toronto, Ontario, Canada
  • Cristoffer Sevilla; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD
  • Thawfeek Mohamed Varusai; Reactome, EMBL-EBI, Cambridge, UK
  • Jean-Marie Ravel; University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, F-54000 Nancy, France.
  • Vera Ortseifen; Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld,
  • Silvia Marchesi; Uppsala University - 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, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
  • Anders Riutta; Gladstone Institutes, Institute for Data Science and Biotechnology, 1650 Owens St., San Francisco, CA 94131, USA
  • Martin Golebiewski; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany)
  • Stuart Owen; The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK
  • Carole Goble; The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK
  • Xiaoming Hu; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany)
  • Rupert Overall; German Center for Neurodegenerative Diseases (DZNE) Dresden, Tatzberg 41, 01307 Dresden, Germany.
  • Dieter Maier; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
  • Angela Bauch; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
  • Benjamin M Gyori; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA
  • John A Bachman; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA
  • Carlos Vega; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
  • Valentin Groues; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
  • Miguel Vazquez; Barcelona Supercomputing Center (BSC), Barcelona, Spain
  • Pablo Porras; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, CB10 1SD, Hinxton, UK
  • Luana Licata; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
  • Marta Iannuccelli; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
  • Francesca Sacco; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy
  • Denes Turei; Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
  • Augustin Luna; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
  • Ozgun Babur; University of Massachusetts Boston, Computer Science Department, 100 William T, Morrissey Blvd, Boston, MA 02125
  • Sylvain Soliman; Inria Saclay Ile-de-France
  • Alberto Valdeolivas; Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
  • Marina Esteban-Medina; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.
  • Maria Pena-Chilet; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.
  • Kinza Rian; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.
  • Tomas Helikar; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA
  • Bhanwar Lal Puniya; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA
  • Anastasia Nesterova; Elsevier, Life Science Department
  • Anton Yuryev; Elsevier, Professional Services, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103
  • Anita de Waard; Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465
  • Dezso Modos; Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
  • Agatha Treveil; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
  • Marton Laszlo Olbei; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
  • Bertrand De Meulder; Association EISBM
  • Aurelien Naldi; Inria Saclay - Ile de France, Lifeware group, 91120 Palaiseau, France
  • Aurelien Dugourd; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
  • Laurence Calzone; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France.
  • Chris Sander; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
  • Emek Demir; Oregon Health and Science University, Department of Molecular and Medical Genetics, 3222 SW Research Drive, Mail Code: L103, Portland, Oregon, U.S.A. 97239
  • Tamas Korcsmaros; Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
  • Tom C Freeman; The Roslin Institute, University of Edinburgh EH25 9RG
  • Franck Auge; Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France
  • Jacques S Beckmann; University of Lausanne, Lausanne, Switzerland
  • Jan Hasenauer; Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany
  • Olaf Wolkenhauer; University of Rostock, Dept of Systems Biology & Bioinformatics
  • Egon 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 Evelo; Dept. Bioinformatics - BiGCaT, Maastricht University, The Netherlands
  • Lincoln D Stein; Ontario Institute for Cancer Research, Adaptive Oncology Theme, 661 University Ave, Toronto, ON M5G 1M1 Canada
  • Henning Hermjakob; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
  • Julio Saez-Rodriguez; Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine, Im Neuenheimer Feld 267, 69120 Heidelberg
  • Joaquin Dopazo; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio. 41013. 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; -
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-356014
ABSTRACT
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. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.
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Texto completo: Disponível Coleções: Preprints Base de dados: bioRxiv Tipo de estudo: Estudo prognóstico Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint
Texto completo
Adicionar na Minha BVS
Imprimir
XML
Buscar no Google
Texto completo: Disponível Coleções: Preprints Base de dados: bioRxiv Tipo de estudo: Estudo prognóstico Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint