publication . Article . Other literature type . 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; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; ...
Open Access English
  • Published: 01 Oct 2021
  • Publisher: HAL CCSD
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.
Funder: Bundesministerium für Bildung und Forschung (BMBF)
Funder: Bundesministerium für Bildung und Forschung
Subjects
free text keywords: computable knowledge repository, large-scale biocuration, omics data analysis, open access community effort, systems biomedicine Subject Categories Computational Biology, Microbiology, Virology & Host Pathogen Interaction, [SDV]Life Sciences [q-bio], Article, Articles, large‐scale biocuration, systems biomedicine, Computational Biology, Microbiology, Virology & Host Pathogen Interaction, computable knowledge repository, large-scale biocuration, omics data analysis, open access community effort, systems biomedicine, Biochemistry and Molecular Biology, Biokemi och molekylärbiologi, BETA, CORONAVIRUS, DEGRADATION, ENVIRONMENT, EXPRESSION, INTERFERON SIGNALING PATHWAY, NF-KAPPA-B, SARS-COV, SARS-COV-2, SPIKE PROTEIN, Applied Mathematics, Computational Theory and Mathematics, General Agricultural and Biological Sciences, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, Information Systems, EMBO10, EMBO23, : Biotechnology [F06] [Life sciences], : Biotechnologie [F06] [Sciences du vivant], : Multidisciplinary, general & others [F99] [Life sciences], : Multidisciplinaire, généralités & autres [F99] [Sciences du vivant], : Immunology & infectious disease [D12] [Human health sciences], : Immunologie & maladie infectieuse [D12] [Sciences de la santé humaine], : Multidisciplinary, general & others [D99] [Human health sciences], : Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], computable knowledge repository; large-scale biocuration; omics data analysis; open access community effort; systems biomedicine, Corrigendum, Biology (General), QH301-705.5, Medicine (General), R5-920, :Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], COVID-19 (Disease), Repositories, Digital, Datasets, COVID-19 (Malaltia), EMBO10, EMBO23, Article, Articles, large‐scale biocuration, ddc:004, Network analysis, Data science, Key (cryptography), Domain (software engineering), Computational resource, Systems biomedicine, Interoperability, Representation (systemics), Graph (abstract data type), Biology
Communities
Funded by
EC| INFORE
Project
INFORE
Interactive Extreme-Scale Analytics and Forecasting
  • Funder: European Commission (EC)
  • Project Code: 825070
  • Funding stream: H2020 | RIA
,
EC| PerMedCoE
Project
PerMedCoE
HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE
  • Funder: European Commission (EC)
  • Project Code: 951773
  • Funding stream: H2020 | RIA
,
EC| iPLACENTA
Project
iPLACENTA
Innovation in modelling Placenta for Maternal and Fetal Health
  • Funder: European Commission (EC)
  • Project Code: 765274
  • Funding stream: H2020 | MSCA-ITN-ETN
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