COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Abstract

COMMEnTOPEn 2 Scientific Data | (2020) 7:136 | https://doi.), an effort to build a comprehensive, standardized knowledge repository of SARS-CoV-2 virus-host interaction mechanisms, guided by input from domain experts and based on published work. This knowledge, available in the vast body of existing literature 1,2 and the fast-growing number of new SARS-CoV-2 publications, needs rigorous and efficient organization in both human and machine-readable formats.This endeavour is an open collaboration between clinical researchers, life scientists, pathway curators, computational biologists and data scientists. Currently, 162 contributors from 25 countries around the world are participating in the project, including partners from Reactome 3 , WikiPathways 4 , IMEx Consortium 5 , Pathway Commons 6 , DisGeNET 7 , ELIXIR 8 , and the Disease Maps Community 9 . With this effort, we aim for long-term community-based development of high-quality models and knowledge bases, linked to data repositories.The COVID-19 Disease Map will be a platform for visual exploration and computational analyses of molecular processes involved in SARS-CoV-2 entry, replication, and host-pathogen interactions, as well as immune response, host cell recovery and repair mechanisms. The map will support the research community and improve our understanding of this disease to facilitate the development of efficient diagnostics and therapies. Figure 1 illustrates the initial scope and layout of the map and its life cycle.At the time this Comment went to press, the COVID-19 Disease Map contains pathways of (i) the virus replication cycle and its transcription mechanisms; (ii) SARS-CoV-2 impact on ACE2-regulated pulmonary blood pressure, apoptosis, Cul2-mediated ubiquitination, heme catabolism, Interferon 2 and PAMP signalling, and endoplasmic reticulum stress; (iii) SARS-CoV-2 proteins Nsp4, Nsp6, Nsp14 and Orf3a. Moreover, the map incorporates the COVID-19 collection of WikiPathway diagrams 10 and a pre-published genome-scale metabolic model of human alveolar macrophages with SARS-CoV-2 11 . All these contributed open-access resources are referenced at https://fairdomhub.org/projects/190#models.By combining diagrammatic representation of COVID-19 mechanisms with underlying models, the map fulfils a dual role. First, it is a graphical, interactive representation of disease-relevant molecular mechanisms linking different knowledge bases. Second, it is a computational resource of reviewed content for graph-based analyses 12 and disease modelling 13 . Thus, it provides a platform for domain experts, such as clinicians, virologists, and immunologists, to collaborate with data scientists and computational biologists for a rigorous model building, accurate data interpretation and drug repositioning. It offers a shared mental map to understand gender, age, and other susceptibility features of the host, disease progression, defence mechanisms, and response to treatment. Finally, it can be used together with the maps of other human diseases to study comorbidities.In...

Perspectives on Platelet Heterogeneity and Host Immune Response in Coronavirus Disease 2019 (COVID-19)

“…To this end, quantitative phosphoproteomics profiling and pathway mapping may offer a means to define platelet phenotypes in specific contexts, 51 and collaborative efforts such as the COVID-19 Disease Map Initiative may help to specify molecular features of platelet phenotypes in COVID-19. 52 Regardless of current and future prospects of defining biomarkers and platelet phenotypes specific to COVID-19, several lines of evidence point to platelets as important regulators of dysregulated inflammation and coagulation in COVID-19. Ongoing and future studies of platelets in inflammation and COVID-19 will better determine whether and how platelet function is beneficial and detrimental to, as well as informative of, disease progression and outcomes in SARS-CoV-2 infection.…”

The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents

“…This technology is a platform that contributes to the computational analysis of molecular processes involved in the 2019-nCoC input and replication interactions in the host. Besides, information about the immune system’s performance, recovery of host cells, and repair mechanisms can be obtained through the COVID-19 Disease Map [ 137 ]. Figure 8 demonstrates the objective and the initial layout of the map and its operating cycle.…”

“…According to the creators of the technology, the content inserted in the COVID-19 Disease Map is selected and reviewed from databases and knowledge continuously. This update is carried out according to the materials available in databases on the subject to support visual and computational exploration, as well as efforts to model diseases [ 137 ]. Note: This image was developed using the CorelDraw software (2017 Corel Corporation ID 410003).…”

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