COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Authors: Ostaszewski Marek , Niarakis Anna , Mazein Alexander , Kuperstein Inna , Phair Robert , Orta-Resendiz Aurelio , Singh Vidisha , Aghamiri Sara Sadat , Acencio Marcio Luis , Glaab Enrico , Ruepp Andreas , Fobo Gisela , Montrone Corinna , Brauner Barbara , Frishman Goar , Cristóbal Monraz Gómez Luis , Somers Julia , Hoch Matti , Gupta Shailendra Kumar , Scheel Julia , Borlinghaus Hanna , Czauderna Tobias , Schreiber Falk , Montagud Arnau , Leon Miguel Ponce de , Funahashi Akira , Hiki Yusuke , Hiroi Noriko , Yamada Takahiro G. , Dräger Andreas , Renz Alina , Naveez Muhammad , Bocskei Zsolt , Messina Francesco , Börnigen Daniela , Fergusson Liam , Conti Marta , Rameil Marius , Nakonecnij Vanessa , Vanhoefer Jakob , Schmiester Leonard , Wang Muying , Ackerman Emily E. , Shoemaker Jason , Zucker Jeremy , Oxford Kristie , Teuton Jeremy , Kocakaya Ebru , Yağmur Summak Gökçe , Hanspers Kristina , Kutmon Martina , Coort Susan , Eijssen Lars , Ehrhart Friederike , Rex D. A. B. , Slenter Denise , Martens Marvin , Pham Nhung , Haw Robin , Jassal Bijay , Matthews Lisa , Orlic-Milacic Marija , Ribeiro Andrea Senff , Rothfels Karen , Shamovsky Veronica , Stephan Ralf , Sevilla Cristoffer , Varusai Thawfeek , Ravel Jean-Marie , Fraser Rupsha , Ortseifen Vera , Marchesi Silvia , Gawron Piotr , Smula Ewa , Heirendt Laurent , Satagopam Venkata , Wu Guanming , Riutta Anders , Golebiewski Martin , Owen Stuart , Goble Carole , Hu Xiaoming , Overall Rupert W. , Maier Dieter , Bauch Angela , Gyori Benjamin M. , Bachman John A. , Vega Carlos , Grouès Valentin , Vazquez Miguel , Porras Pablo , Licata Luana , Iannuccelli Marta , Sacco Francesca , Nesterova Anastasia , Yuryev Anton , Waard Anita de , Turei Denes , Luna Augustin , Babur Ozgun , Soliman Sylvain , Valdeolivas Alberto , Medina Marina Esteban- , Peña-Chilet Maria , Rian Kinza , Helikar Tomáš , Puniya Bhanwar Lal , Modos Dezso , Treveil Agatha , Olbei Marton , Meulder Bertrand De , Dugourd Aurélien , Naldi Aurélien , Noë Vincent , Calzone Laurence , Sander Chris , Demir Emek , Korcsmaros Tamas , Freeman Tom C. , Augé Franck , Beckmann Jacques S. , Hasenauer Jan , Wolkenhauer Olaf , Wilighagen Egon L. , Pico Alexander R. , Evelo Chris T. , Gillespie Marc E. , Stein Lincoln D. , Hermjakob Henning , D’Eustachio Peter , Saez-Rodriguez Julio , Dopazo Joaquin , Valencia Alfonso , Kitano Hiroaki , Barillot Emmanuel , Auffray Charles , Balling Rudi , Schneider Reinhard ,   the COVID-19 Disease Map Community
Published: October 2020

AbstractWe 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.