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Journal Articles Molecular Systems Biology Year : 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 (1) , 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 Ya Gmur 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 (2) , 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 Wilighagen , 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 , Covid-19 Disease Map Community
Marek Ostaszewski
  • Function : Correspondent author
  • PersonId : 1138223

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Anna Niarakis
Alexander Mazein
Inna Kuperstein
Robert Phair
Aurelio Orta-Resendiz
Sara Sadat Aghamiri
Marcio Luis Acencio
Enrico Glaab
Andreas Ruepp
Gisela Fobo
  • Function : Author
Corinna Montrone
  • Function : Author
Barbara Brauner
  • Function : Author
Goar Frishman
  • Function : Author
Luis Cristóbal Monraz Gómez
  • Function : Author
Julia Somers
Matti Hoch
Shailendra Kumar Gupta
Julia Scheel
Hanna Borlinghaus
  • Function : Author
Tobias Czauderna
Falk Schreiber
  • Function : Author
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
  • Function : Author
Marta Conti
  • Function : Author
Marius Rameil
Vanessa Nakonecnij
  • Function : Author
Jakob Vanhoefer
Leonard Schmiester
Muying Wang
  • Function : Author
Emily E Ackerman
Jason E Shoemaker
Jeremy Zucker
Kristie Oxford
Jeremy Teuton
Ebru Kocakaya
Gökçe Ya Gmur Summak
Kristina Hanspers
Martina Kutmon
Susan Coort
Lars Eijssen
Friederike Ehrhart
Devasahayam Arokia
  • Function : Author
Balaya Rex
Denise Slenter
Marvin Martens
Nhung Pham
Robin Haw
Bijay Jassal
Lisa Matthews
Marija Orlic-Milacic
Andrea Senff Ribeiro
Karen Rothfels
Veronica Shamovsky
  • Function : Author
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
  • Function : Author
Angela Bauch
Benjamin M Gyori
John A Bachman
Carlos Vega
Valentin Grouès
Miguel Vazquez
Pablo Porras
Luana Licata
Marta Iannuccelli
  • Function : Author
Francesca Sacco
Anastasia Nesterova
Anton Yuryev
  • Function : Author
Anita de Waard
Denes Turei
Augustin Luna
Ozgun Babur
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
  • Function : Author
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 Wilighagen
Alexander R Pico
Chris T Evelo
Marc E Gillespie
Lincoln D Stein
Henning Hermjakob
Peter d'Eustachio
Julio Saez-Rodriguez
Joaquin Dopazo
  • Function : Author
Alfonso Valencia
  • Function : Author
Hiroaki Kitano
  • Function : Author
Emmanuel Barillot
Charles Auffray
  • Function : Author
Rudi Balling
  • Function : Author
Reinhard Schneider
  • Function : Author
Covid-19 Disease Map Community
  • Function : Author

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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Dates and versions

hal-03385317 , version 1 (24-02-2021)
hal-03385317 , version 2 (19-10-2021)

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Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, et al.. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩. ⟨hal-03385317v2⟩
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