TY - JOUR
T1 - COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
AU - Ostaszewski, Marek
AU - Niarakis, Anna
AU - Mazein, Alexander
AU - Kuperstein, Inna
AU - Phair, Robert
AU - Orta-Resendiz, Aurelio
AU - Singh, Vidisha
AU - Aghamiri, Sara Sadat
AU - Acencio, Marcio Luis
AU - Glaab, Enrico
AU - Ruepp, Andreas
AU - Fobo, Gisela
AU - Montrone, Corinna
AU - Brauner, Barbara
AU - Frishman, Goar
AU - Monraz Gómez, Luis Cristóbal
AU - Somers, Julia
AU - Hoch, Matti
AU - Kumar Gupta, Shailendra
AU - Scheel, Julia
AU - Borlinghaus, Hanna
AU - Czauderna, Tobias
AU - Schreiber, Falk
AU - Montagud, Arnau
AU - Ponce de Leon, Miguel
AU - Funahashi, Akira
AU - Hiki, Yusuke
AU - Hiroi, Noriko
AU - Yamada, Takahiro G
AU - Dräger, Andreas
AU - Renz, Alina
AU - Naveez, Muhammad
AU - Bocskei, Zsolt
AU - Messina, Francesco
AU - Börnigen, Daniela
AU - Fergusson, Liam
AU - Conti, Marta
AU - Rameil, Marius
AU - Nakonecnij, Vanessa
AU - Vanhoefer, Jakob
AU - Schmiester, Leonard
AU - Wang, Muying
AU - Kutmon, Martina
AU - Coort, Susan
AU - Eijssen, Lars
AU - Ehrhart, Friederike
AU - Slenter, Denise
AU - Martens, Marvin
AU - Pham, Nhung
AU - Evelo, Chris T
AU - COVID-19 Disease Map Community
PY - 2021/10
Y1 - 2021/10
N2 - 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.
AB - 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.
KW - BETA
KW - CORONAVIRUS
KW - DEGRADATION
KW - ENVIRONMENT
KW - EXPRESSION
KW - INTERFERON SIGNALING PATHWAY
KW - NF-KAPPA-B
KW - SARS-COV
KW - SARS-COV-2
KW - SPIKE PROTEIN
KW - computable knowledge repository
KW - large-scale biocuration
KW - omics data analysis
KW - open access community effort
KW - systems biomedicine
U2 - 10.15252/msb.202110387
DO - 10.15252/msb.202110387
M3 - Article
C2 - 34664389
SN - 1744-4292
VL - 17
JO - Molecular Systems Biology
JF - Molecular Systems Biology
IS - 10
M1 - e10387
ER -