COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

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 acces...

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Autores principales:	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 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, the COVID‐19 Disease Map Community
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	computable knowledge repository large‐scale biocuration omics data analysis open access community effort systems biomedicine Biology (General) QH301-705.5 Medicine (General) R5-920
Acceso en línea:	https://doaj.org/article/07d2352966634fc58ef9a394d1092d67
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spelling	oai:doaj.org-article:07d2352966634fc58ef9a394d1092d672021-11-11T11:30:47ZCOVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms1744-429210.15252/msb.202110387https://doaj.org/article/07d2352966634fc58ef9a394d1092d672021-10-01T00:00:00Zhttps://doi.org/10.15252/msb.202110387https://doaj.org/toc/1744-4292Abstract 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.Marek OstaszewskiAnna NiarakisAlexander MazeinInna KupersteinRobert PhairAurelio Orta‐ResendizVidisha SinghSara Sadat AghamiriMarcio Luis AcencioEnrico GlaabAndreas RueppGisela FoboCorinna MontroneBarbara BraunerGoar FrishmanLuis Cristóbal Monraz GómezJulia SomersMatti HochShailendra Kumar GuptaJulia ScheelHanna BorlinghausTobias CzaudernaFalk SchreiberArnau MontagudMiguel Ponce de LeonAkira FunahashiYusuke HikiNoriko HiroiTakahiro G YamadaAndreas DrägerAlina RenzMuhammad NaveezZsolt BocskeiFrancesco MessinaDaniela BörnigenLiam FergussonMarta ContiMarius RameilVanessa NakonecnijJakob VanhoeferLeonard SchmiesterMuying WangEmily E AckermanJason E ShoemakerJeremy ZuckerKristie OxfordJeremy TeutonEbru KocakayaGökçe Yağmur SummakKristina HanspersMartina KutmonSusan CoortLars EijssenFriederike EhrhartDevasahayam Arokia Balaya RexDenise SlenterMarvin MartensNhung PhamRobin HawBijay JassalLisa MatthewsMarija Orlic‐MilacicAndrea Senff RibeiroKaren RothfelsVeronica ShamovskyRalf StephanCristoffer SevillaThawfeek VarusaiJean‐Marie RavelRupsha FraserVera OrtseifenSilvia MarchesiPiotr GawronEwa SmulaLaurent HeirendtVenkata SatagopamGuanming WuAnders RiuttaMartin GolebiewskiStuart OwenCarole GobleXiaoming HuRupert W OverallDieter MaierAngela BauchBenjamin M GyoriJohn A BachmanCarlos VegaValentin GrouèsMiguel VazquezPablo PorrasLuana LicataMarta IannuccelliFrancesca SaccoAnastasia NesterovaAnton YuryevAnita de WaardDenes TureiAugustin LunaOzgun BaburSylvain SolimanAlberto ValdeolivasMarina Esteban‐MedinaMaria Peña‐ChiletKinza RianTomáš HelikarBhanwar Lal PuniyaDezso ModosAgatha TreveilMarton OlbeiBertrand De MeulderStephane BallereauAurélien DugourdAurélien NaldiVincent NoëlLaurence CalzoneChris SanderEmek DemirTamas KorcsmarosTom C FreemanFranck AugéJacques S BeckmannJan HasenauerOlaf WolkenhauerEgon L WilighagenAlexander R PicoChris T EveloMarc E GillespieLincoln D SteinHenning HermjakobPeter D'EustachioJulio Saez‐RodriguezJoaquin DopazoAlfonso ValenciaHiroaki KitanoEmmanuel BarillotCharles AuffrayRudi BallingReinhard Schneiderthe COVID‐19 Disease Map CommunityWileyarticlecomputable knowledge repositorylarge‐scale biocurationomics data analysisopen access community effortsystems biomedicineBiology (General)QH301-705.5Medicine (General)R5-920ENMolecular Systems Biology, Vol 17, Iss 10, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	computable knowledge repository large‐scale biocuration omics data analysis open access community effort systems biomedicine Biology (General) QH301-705.5 Medicine (General) R5-920
spellingShingle	computable knowledge repository large‐scale biocuration omics data analysis open access community effort systems biomedicine Biology (General) QH301-705.5 Medicine (General) R5-920 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 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 the COVID‐19 Disease Map Community COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
description	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.
format	article
author	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 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 the COVID‐19 Disease Map Community
author_facet	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 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 the COVID‐19 Disease Map Community
author_sort	Marek Ostaszewski
title	COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
title_short	COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
title_full	COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
title_fullStr	COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
title_full_unstemmed	COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
title_sort	covid19 disease map, a computational knowledge repository of virus–host interaction mechanisms
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/07d2352966634fc58ef9a394d1092d67
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covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT dezsomodos covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT agathatreveil covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT martonolbei covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT bertranddemeulder covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT stephaneballereau covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT aureliendugourd covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT aureliennaldi covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT vincentnoel covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT laurencecalzone covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT chrissander covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT emekdemir covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT tamaskorcsmaros covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT tomcfreeman covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT franckauge covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT jacquessbeckmann covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT janhasenauer covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT olafwolkenhauer covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT egonlwilighagen covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT alexanderrpico covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT christevelo covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT marcegillespie covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT lincolndstein covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT henninghermjakob covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT peterdeustachio covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT juliosaezrodriguez covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT joaquindopazo covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT alfonsovalencia covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT hiroakikitano covid19diseasemapacomputationalknowledgerepositoryofvirushostinteractionmechanisms AT emmanuelbarillot 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COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

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