ViruSurf: an integrated database to investigate viral sequences

Canakoglu, Arif; Pinoli, Pietro; Bernasconi, Anna; Alfonsi, Tommaso; Melidis, Damianos P.; Ceri, Stefano

doi:10.1093/nar/gkaa846

Cited by 40 publications

(43 citation statements)

References 24 publications

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“…They have created a specific resource for SARS-CoV-2 (https://www. ncbi.nlm.nih.gov/labs/virus/vssi/#/sars-cov-2), the virus responsible for COVID-19, with simple map-based visualization.A platform that provides much more data of this kind, as it integrates different data sources, is ViruSurf [52], which characterizes its sequences by using location information (e.g., continent, country, region, and municipality, when available). Other well-known players of virology bioinformatics have contributed with a geo-spatial analysis on important mutations, such as the D614G variant on the Spike protein [53]; variant distributions in the world ( [54,55]), and the COVID-19 virus mutation tracker (https://www.cbrc.kaust.edu.sa/covmt/index.php?p=maps).…”

Section: The Case Of Genomic and Clinical Geo-oedvmentioning

confidence: 99%

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

Bernasconi

Grandi

2021

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Responding to the recent COVID-19 outbreak, several organizations and private citizens considered the opportunity to design and publish online explanatory data visualization tools for the communication of disease data supported by a spatial dimension. They responded to the need of receiving instant information arising from the broad research community, the public health authorities, and the general public. In addition, the growing maturity of information and mapping technologies, as well as of social networks, has greatly supported the diffusion of web-based dashboards and infographics, blending geographical, graphical, and statistical representation approaches. We propose a broad conceptualization of Web visualization tools for geo-spatial information, exceptionally employed to communicate the current pandemic; to this end, we study a significant number of publicly available platforms that track, visualize, and communicate indicators related to COVID-19. Our methodology is based on (i) a preliminary systematization of actors, data types, providers, and visualization tools, and on (ii) the creation of a rich collection of relevant sites clustered according to significant parameters. Ultimately, the contribution of this work includes a critical analysis of collected evidence and an extensive modeling effort of Geo-Online Exploratory Data Visualization (Geo-OEDV) tools, synthesized in terms of an Entity-Relationship schema. The COVID-19 pandemic outbreak has offered a significant case to study how and how much modern public communication needs spatially related data and effective implementation of tools whose inspection can impact decision-making at different levels. Our resulting model will allow several stakeholders (general users, policy-makers, and researchers/analysts) to gain awareness on the assets of structured online communication and resource owners to direct future development of these important tools.

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Section: The Case Of Genomic and Clinical Geo-oedvmentioning

confidence: 99%

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

Bernasconi

Grandi

2021

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“…ViruSurf [ 53 ] ( http://gmql.eu/virusurf/ ), dual of the human genomics search engine GenoSurf [ 54 ], is based on a conceptual model [ 31 ] that describes sequences and their metadata from their biological, technical, organizational and analytical perspectives. It provides many options for building search queries, by combining—within rich Boolean expressions—metadata attributes about viral sequences and nucleotide and amino acid variants.…”

Section: Sars-cov2 Search Systemsmentioning

confidence: 99%

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

Bernasconi

Canakoglu

Masseroli

et al. 2020

Briefings in Bioinformatics

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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.

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“…In this respect, we underscore that any initiative aiming to apply well established standards and protocols for the sharing of SARS-CoV-2 genetic/genomic data, like for example the application or modification of the Beacon [ 130 ] protocol, as available from [ 131 ] should be fully supported by the SARS-CoV-2 research community. Finally, we stress the importance of developing highly curated resources and databases to allow the seamless integration of different types of data/and or the execution of complex queries, which could represent an important added value for data mining and meta-analyses, as exemplified by [ 132 ]. By allowing the seamless and rapid integration of different types of data and metadata, these and similar resources can—at least in part—mitigate some of the most important limitations for a rapid and widespread access to the COVID-19 data.…”

Section: Data Analysis Deposition and Accessmentioning

confidence: 99%

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Chiara

D’Erchia

Gissi

et al. 2020

Briefings in Bioinformatics

161

153

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Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘ vademecum ’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.

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ViruSurf: an integrated database to investigate viral sequences

Cited by 40 publications

References 24 publications

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

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

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

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

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