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Empowering Virus Sequence Research Through Conceptual Modeling

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Conceptual Modeling (ER 2020)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 12400))

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Abstract

The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations, nucleotide and amino acid variants), organizational (sequencing project) and technical (experimental technology).

VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV-2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research.

Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information.

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Notes

  1. 1.

    SARS-CoV-2 is generally identified by the NCBI taxonomy  [18] ID 2697049.

  2. 2.

    GenoSurf: http://gmql.eu/genosurf/; ViruSurf: http://gmql.eu/virusurf/.

  3. 3.

    http://www.insdc.org/.

  4. 4.

    https://www.ebi.ac.uk/ena/pathogens/.

  5. 5.

    https://4virology.net/virology-ca-tools/vgo/.

  6. 6.

    NGDC: https://bigd.big.ac.cn/; CNGB: https://db.cngb.org/.

  7. 7.

    http://clinicaltrials.gov/.

  8. 8.

    In RNA sequencing databases uracil (U) is replaced with thymine (T).

  9. 9.

    https://www.ncbi.nlm.nih.gov/pubmed/.

  10. 10.

    https://www.ncbi.nlm.nih.gov/bioproject/.

  11. 11.

    https://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation.

  12. 12.

    It represents the positive-sense, single-stranded RNA virus (from 0 to the 29903\(^{th}\) base) of NC_045512 RefSeq staff-curated complete sequence (StrainName “Wuhan-Hu-1”), collected in China from a “Homo Sapiens” HostSample in December 2019.

  13. 13.

    http://glue-tools.cvr.gla.ac.uk/images/projectModel.png.

  14. 14.

    https://www.covid19hg.org/.

  15. 15.

    We coordinated about 50 active participants and released the “Freeze 1” version of the data dictionary on April 16, 2020 (http://gmql.eu/phenotype/).

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Acknowledgements

This research is funded by the ERC Advanced Grant 693174 GeCo (Data-Driven Genomic Computing), 2016–2021. The authors would like to thank Ilaria Capua, Luca Ferretti, Alice Fusaro, Susanna Lamers, Francesca Mari, Carla Mavian, Alessandra Renieri, Stephen Tsui, and Limsoon Wong for their precious contributions during the phase of requirements elicitation and for their inspiration towards future developments of this research.

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Authors and Affiliations

  1. Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133, Milano, Italy

    Anna Bernasconi, Arif Canakoglu, Pietro Pinoli & Stefano Ceri

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  1. Anna Bernasconi
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  2. Arif Canakoglu
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  3. Pietro Pinoli
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  4. Stefano Ceri
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Corresponding author

Correspondence to Anna Bernasconi .

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Editors and Affiliations

  1. University of Auckland, Auckland, New Zealand

    Gillian Dobbie

  2. University of Duisburg-Essen, Essen, Germany

    Ulrich Frank

  3. TU Wien, Vienna, Austria

    Gerti Kappel

  4. Brigham Young University, Provo, UT, USA

    Stephen W. Liddle

  5. University of Klagenfurt, Klagenfurt am Wörthersee, Austria

    Heinrich C. Mayr

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Bernasconi, A., Canakoglu, A., Pinoli, P., Ceri, S. (2020). Empowering Virus Sequence Research Through Conceptual Modeling. In: Dobbie, G., Frank, U., Kappel, G., Liddle, S.W., Mayr, H.C. (eds) Conceptual Modeling. ER 2020. Lecture Notes in Computer Science(), vol 12400. Springer, Cham. https://doi.org/10.1007/978-3-030-62522-1_29

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  • DOI: https://doi.org/10.1007/978-3-030-62522-1_29

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