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ViruSurf

General Information

ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola, and Dengue. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

Homepage http://gmql.eu/virusurf/

Countries that developed this resource Italy

Created in 2020

Taxonomic range

Knowledge Domains

Subjects

User-defined Tags

COVID-19

How to cite this record FAIRsharing.org: ViruSurf; ViruSurf; DOI: https://doi.org/10.25504/FAIRsharing.vx5OEv; Last edited: Jan. 25, 2021, 4:28 p.m.; Last accessed: Aug 02 2021 12:56 a.m.

Publication for citation ViruSurf: an integrated database to investigate viral sequences. Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S; Nucleic Acids Res ; 2020; https://doi.org/10.1093/nar/gkaa846;

This record is maintained by acanak

Record added: Sept. 18, 2020, 12:41 p.m.
Record updated: Nov. 4, 2020, 12:02 p.m. by acanak.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.vx5OEv' by 'acanak' at 09:27, 26 Oct 2020 (approved):

	'publications' has been modified:
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			ViruSurf: an integrated database to investigate viral sequences.|Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S|Nucleic Acids Res|2020
		Added:
			ViruSurf: an integrated database to investigate viral sequences.|Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S|Nucleic Acids Res|2020
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Edits to 'https://fairsharing.org/FAIRsharing.vx5OEv' by 'The FAIRsharing Team' at 14:12, 01 Oct 2020 (approved):

	'user_defined_tags' has been modified:
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			COVID-19
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			COVID-19
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			help|https://www.youtube.com/watch?v=ljo4WWZ1rU0&list=PLfWxoOMC6swIkqfLc3G4H-hW_pdmI1jFF
			online documentation|https://github.com/DEIB-GECO/vue-metadata/wiki
		Added:
			help|https://www.youtube.com/watch?v=ljo4WWZ1rU0&list=PLfWxoOMC6swIkqfLc3G4H-hW_pdmI1jFF
			online documentation|https://github.com/DEIB-GECO/vue-metadata/wiki
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	'onto_disciplines' has been modified:
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			Data Integration
			Data Management
			Data Quality
			Data Visualization
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			Data Integration
			Data Management
			Data Quality
			Data Visualization
			Life Science
			Microbiology
			Virology
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			Life Science
			Microbiology
			Virology
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	'dataProcesses' has been modified:
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			Curation principles, data curation, http://geco.deib.polimi.it/virusurf/repo_static/datacuration.html
			Search & browse, data access, http://geco.deib.polimi.it/virusurf/
			Search & Browse Sequences of the virus responsible for COVID-19, data access, http://geco.deib.polimi.it/virusurf_gisaid/
		Added:
			Curation principles, data curation, http://geco.deib.polimi.it/virusurf/repo_static/datacuration.html
			Search & browse, data access, http://geco.deib.polimi.it/virusurf/
			Search & Browse Sequences of the virus responsible for COVID-19, data access, http://geco.deib.polimi.it/virusurf_gisaid/
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Edits to 'https://fairsharing.org/FAIRsharing.vx5OEv' by 'The FAIRsharing Team' at 11:03, 28 Sep 2020 (approved):

'doi' has been modified:
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'miriam_id' has been modified:
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After: None

'description' has been modified:
Before: ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola, and Dengue. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

After: ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola, and Dengue. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

Edits to 'https://fairsharing.org/FAIRsharing.vx5OEv' by 'acanak' at 13:16, 18 Sep 2020 (approved):

	'related_databases' has been modified:
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			GenBank
			GISAID EpiCoV Database
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			GenBank
			Reference Sequence Database
			GISAID EpiCoV Database
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			Reference Sequence Database
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Edits to 'https://fairsharing.org/FAIRsharing.vx5OEv' by 'acanak' at 13:03, 18 Sep 2020 (approved):

	'related_databases' has been modified:
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			GenBank
			GISAID EpiCoV Database
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			GenBank
			GISAID EpiCoV Database
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			Politecnico di Milano|http://www.bioinformatics.deib.polimi.it/geco/|Maintains
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			Politecnico di Milano|http://www.bioinformatics.deib.polimi.it/geco/|Maintains
			The European Research Council (ERC)|https://erc.europa.eu/|Funds
			European Institute of Innovation & Technology (EIT)|https://eit.europa.eu/|Funds
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			The European Research Council (ERC)|https://erc.europa.eu/|Funds
			European Institute of Innovation & Technology (EIT)|https://eit.europa.eu/|Funds
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			20663
			ERC Advanced Grant 693174
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			20663
			ERC Advanced Grant 693174
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	'onto_disciplines' has been modified:
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			Data Integration
			Data Management
			Data Quality
			Data Visualization
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			Data Integration
			Data Management
			Data Quality
			Data Visualization
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	'onto_domains' has been modified:
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			data representational model
			mutation
			mutation analysis
			variant
			viral_sequence
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			data representational model
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			mutation analysis
			variant
			viral_sequence
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In Collections

COVID-19 Resources

Support

General

help	Video Presentation
online documentation	GitHub

Additional Information

Contact

Arif Canakoglu ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Data Curation

Curation principles

http://geco.deib.polimi.it/virusurf/repo_static/datacuration.html

Data Access

Search & browse	http://geco.deib.polimi.it/virusurf/
Search & Browse Sequences of the virus responsible for COVID-19	http://geco.deib.polimi.it/virusurf_gisaid/

Publications

ViruSurf: an integrated database to investigate viral sequences.

Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S
Nucleic Acids Res 2020

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by acanak

Funds

The European Research Council (ERC) (Government body)
European Institute of Innovation & Technology (EIT)

Maintains

Politecnico di Milano (University) Lead

Grant Number(s)

20663 (European Institute of Innovation & Technology (EIT))
ERC Advanced Grant 693174 (The European Research Council (ERC))

ViruSurf

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