A review on viral data sources and search systems for perspective mitigation of COVID-19

Abstract

With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the effects of the pandemic. In this context, we review the data integration efforts required for accessing and searching genome sequences and metadata of SARS-CoV2, the virus responsible for the COVID-19 disease, which have been deposited into the most important repositories of viral sequences. Organizations that were already present in the virus domain are now dedicating special interest to the emergence of COVID-19 pandemics, by emphasizing specific SARS-CoV2 data and services. At the same time, novel organizations and resources were born in this critical period to serve specifically the purposes of COVID-19 mitigation while setting the research ground for contrasting possible future pandemics. Accessibility and integration of viral sequence data, possibly in conjunction with the human host genotype and clinical data, are paramount to better understand the COVID-19 disease and mitigate its effects. Few examples of host-pathogen integrated datasets exist so far, but we expect them to grow together with the knowledge of COVID-19 disease; once such datasets will be available, useful integrative surveillance mechanisms can be put in place by observing how common variants distribute in time and space, relating them to the phenotypic impact evidenced in the literature.

A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic

“…Imaging data represent a particular subset of clinical data. A dated conceptual model for this information was proposed in [34] but more recent efforts are arising in the Cancer Genomics practice [35] and in the COVID-19 research community [36], as shown in [37].…”

Ontological Unpacking as Explanation: The Case of the Viral Conceptual Model

“…2 In OntoUML models, we employ the generally-accepted color coding scheme: light red is used for types whose instances are objects, green when instances are relators, yellow when instances are events, and purple when instances are higher-order types. 3 By using the multi-modeling support in UFO/OntoUML, one could proceed further and explicitly capture the relations of subordination between, for example, species and genus, namely, that a type is subordinate to another iff the instances of the former are specializations of instances of the latter [9]. For space reasons, we do not elaborate further.…”

“…The Viral Conceptual Model (VCM) [4] was motivated by interest in representing the genomic aspects of COVID-19 so they can be shared among the scientific and medical communities that are attempting to understand SARS-CoV-2 and similar pathogens. The model is being used for designing: an integrated data warehouse and search system [8]; a linked Phenotype Data Dictionary [3]; a knowledge base of variant impacts [1]; and a visualization engine [6]. To facilitate a further, robust, application of VCM to projects with other viruses and pathogens, there needs to be some way to assess the quality of the model.…”

COVID-19: why not learn from the past?

“…New variants of SARS-Cov2 keep being described [55][56][57][58] and deposited in old, as well as new, dedicated sequence databases (reviewed in [59]). As a measure of the staggering numbers of sequences, GenBank, which is continuously updated from laboratories around the world, had about 300 SARS-CoV-2 nucleotide sequences by the end of March 2020, and 27 660 by October 8, 2020, an almost 100-fold increase in just 6 months.…”