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

doi:10.1038/s41597-020-0477-8

. 2020 May 5;7(1):136.

doi: 10.1038/s41597-020-0477-8.

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

Marek Ostaszewski¹, Alexander Mazein^{1

2}, Marc E Gillespie^{3

4}, Inna Kuperstein⁵, Anna Niarakis⁶, Henning Hermjakob⁷, Alexander R Pico⁸, Egon L Willighagen⁹, Chris T Evelo^{9

10}, Jan Hasenauer^{11

12

13}, Falk Schreiber^{14

15}, Andreas Dräger^{16

17

18}, Emek Demir¹⁹, Olaf Wolkenhauer^{20

21}, Laura I Furlong²², Emmanuel Barillot⁵, Joaquin Dopazo^{23

24

25

26}, Aurelio Orta-Resendiz^{27

28}, Francesco Messina^{29

30}, Alfonso Valencia^{31

32}, Akira Funahashi³³, Hiroaki Kitano^{34

35

36}, Charles Auffray², Rudi Balling¹, Reinhard Schneider³⁷

Affiliations

¹ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
² European Institute for Systems Biology and Medicine (EISBM), Vourles, France.
³ Ontario Institute for Cancer Research, Toronto, Canada.
⁴ College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA.
⁵ Institut Curie, PSL Research University, Mines Paris Tech, Inserm, Paris, France.
⁶ Department of Biology, Univ. Évry, University of Paris-Saclay, Genopole, 91025, Évry, France.
⁷ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
⁸ Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.
⁹ Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
¹⁰ Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands.
¹¹ Helmholtz Zentrum München, Institute of Computational Biology, Neuherberg, Germany.
¹² Center for Mathematics, Technische Universität München, Garching, Germany.
¹³ Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
¹⁴ University of Konstanz, Department of Computer and Information Science, Konstanz, Germany.
¹⁵ Monash University, Faculty of Information Technology, Melbourne, Australia.
¹⁶ Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076, Tübingen, Germany.
¹⁷ Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany.
¹⁸ German Center for Infection Research (DZIF), partner site, Tübingen, Germany.
¹⁹ Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, USA.
²⁰ Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany.
²¹ Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7602, Stellenbosch, South Africa.
²² Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
²³ Clinical Bioinformatics Area, Fundación Progreso y Salud. Hosp. Virgen del Rocío, Sevilla, Spain.
²⁴ Bioinformatics in Rare Diseases. Centro de Investigación Biomédica en Red de Enfermedades Raras, Fundación Progreso y Salud, Hosp. Virgen del Rocío, Sevilla, Spain.
²⁵ INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, 42013, Spain.
²⁶ Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain.
²⁷ HIV, Inflammation and Persistence Unit, Virology Department, Institut Pasteur, Paris, France.
²⁸ Bio Sorbonne Paris Cité, Université de Paris, Paris, France.
²⁹ Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy.
³⁰ COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy.
³¹ Barcelona Supercomputing Center (BSC), Barcelona, Spain.
³² Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.
³³ Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan.
³⁴ The Systems Biology Institute, Shinagawa, Tokyo, Japan.
³⁵ Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan.
³⁶ Sony Computer Science Laboratories, Inc., Tokyo, Japan.
³⁷ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. reinhard.schneider@uni.lu.

PMID: 32371892
PMCID: PMC7200764
DOI: 10.1038/s41597-020-0477-8

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

Marek Ostaszewski et al. Sci Data. 2020.

. 2020 May 5;7(1):136.

doi: 10.1038/s41597-020-0477-8.

Authors

Affiliations

¹ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
² European Institute for Systems Biology and Medicine (EISBM), Vourles, France.
³ Ontario Institute for Cancer Research, Toronto, Canada.
⁴ College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA.
⁵ Institut Curie, PSL Research University, Mines Paris Tech, Inserm, Paris, France.
⁶ Department of Biology, Univ. Évry, University of Paris-Saclay, Genopole, 91025, Évry, France.
⁷ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
⁸ Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.
⁹ Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
¹⁰ Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands.
¹¹ Helmholtz Zentrum München, Institute of Computational Biology, Neuherberg, Germany.
¹² Center for Mathematics, Technische Universität München, Garching, Germany.
¹³ Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
¹⁴ University of Konstanz, Department of Computer and Information Science, Konstanz, Germany.
¹⁵ Monash University, Faculty of Information Technology, Melbourne, Australia.
¹⁶ Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076, Tübingen, Germany.
¹⁷ Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany.
¹⁸ German Center for Infection Research (DZIF), partner site, Tübingen, Germany.
¹⁹ Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, USA.
²⁰ Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany.
²¹ Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7602, Stellenbosch, South Africa.
²² Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
²³ Clinical Bioinformatics Area, Fundación Progreso y Salud. Hosp. Virgen del Rocío, Sevilla, Spain.
²⁴ Bioinformatics in Rare Diseases. Centro de Investigación Biomédica en Red de Enfermedades Raras, Fundación Progreso y Salud, Hosp. Virgen del Rocío, Sevilla, Spain.
²⁵ INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, 42013, Spain.
²⁶ Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain.
²⁷ HIV, Inflammation and Persistence Unit, Virology Department, Institut Pasteur, Paris, France.
²⁸ Bio Sorbonne Paris Cité, Université de Paris, Paris, France.
²⁹ Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy.
³⁰ COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy.
³¹ Barcelona Supercomputing Center (BSC), Barcelona, Spain.
³² Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.
³³ Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan.
³⁴ The Systems Biology Institute, Shinagawa, Tokyo, Japan.
³⁵ Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan.
³⁶ Sony Computer Science Laboratories, Inc., Tokyo, Japan.
³⁷ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. reinhard.schneider@uni.lu.

PMID: 32371892
PMCID: PMC7200764
DOI: 10.1038/s41597-020-0477-8

Erratum in

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Ostaszewski M, et al. Sci Data. 2020 Jul 17;7(1):247. doi: 10.1038/s41597-020-00589-w. Sci Data. 2020. PMID: 32678106 Free PMC article.

Abstract

Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
The overview of the COVID-19 Disease Map project. The map focuses on SARS-CoV-2 replication cycle, its interactions with the host, reaction of the immune system and repair mechanisms. The curated and reviewed content will be continuously integrated and cross-linked with data and knowledge bases, to support visual and computational exploration, as well as disease modelling efforts. The acquired results will benefit the research community and provide feedback to refine the scope of curation activities.

See this image and copyright information in PMC

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References

1. Fung TS, Liu DX. Human Coronavirus: Host-Pathogen Interaction. Annu. Rev. Microbiol. 2019;73:529–557. doi: 10.1146/annurev-micro-020518-115759. - DOI - PubMed
1. 2020. COVID-19 Open Research Dataset (CORD-19). Semantic Scholar. https://pages.semanticscholar.org/coronavirus-research
1. Jassal B, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2020;48:D498–D503. - PMC - PubMed
1. Slenter DN, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 2018;46:D661–D667. doi: 10.1093/nar/gkx1064. - DOI - PMC - PubMed
1. Orchard S, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods. 2012;9:345–350. doi: 10.1038/nmeth.1931. - DOI - PMC - PubMed

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[1] Fung TS, Liu DX. Human Coronavirus: Host-Pathogen Interaction. Annu. Rev. Microbiol. 2019;73:529–557. doi: 10.1146/annurev-micro-020518-115759. - DOI - PubMed

[2] Fung TS, Liu DX. Human Coronavirus: Host-Pathogen Interaction. Annu. Rev. Microbiol. 2019;73:529–557. doi: 10.1146/annurev-micro-020518-115759. - DOI - PubMed

[3] 2020. COVID-19 Open Research Dataset (CORD-19). Semantic Scholar. https://pages.semanticscholar.org/coronavirus-research

[4] 2020. COVID-19 Open Research Dataset (CORD-19). Semantic Scholar. https://pages.semanticscholar.org/coronavirus-research

[5] Jassal B, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2020;48:D498–D503. - PMC - PubMed

[6] Jassal B, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2020;48:D498–D503. - PMC - PubMed

[7] Slenter DN, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 2018;46:D661–D667. doi: 10.1093/nar/gkx1064. - DOI - PMC - PubMed

[8] Slenter DN, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 2018;46:D661–D667. doi: 10.1093/nar/gkx1064. - DOI - PMC - PubMed

[9] Orchard S, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods. 2012;9:345–350. doi: 10.1038/nmeth.1931. - DOI - PMC - PubMed

[10] Orchard S, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods. 2012;9:345–350. doi: 10.1038/nmeth.1931. - DOI - PMC - PubMed

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

Affiliations

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

Authors

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Erratum in

Abstract

Conflict of interest statement

Figures

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Erratum in

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Conflict of interest statement

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