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 and 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-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research.
In addition to VCM, we also illustrate the data dictionary for patient’s phenotype used by the COVID-19 Host Genetic Initiative. 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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
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One of the author's last names was misspelled in the paper pdf.
1 SARS-CoV2 is generally identified by the NCBI taxonomy ID 2697049, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049.
2 META-BASE is available at https://github.com/DEIB-GECO/Metadata-Manager.
11 In RNA sequencing databases uracil (U) is replaced with thymine (T).
15 We coordinated about 50 active participants and produced Freeze-1 of the data dictionary, released on April 16, 2020, available at http://gmql.eu/phenotype/.
16 It represents the positive-sense, single-stranded RNA virus (from 0 to the 29903th base) of NC 045512 RefSeq complete sequence (StrainName “Wuhan-Hu-1”), collected in China from a “Homo Sapiens” HostSample in December 2019; it has been curated by NCBI staff.