VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.
Animals
Apicomplexa
/ classification
Bacteria
/ classification
Communicable Diseases
/ microbiology
Computational Biology
/ methods
Data Mining
/ methods
Databases, Factual
Diplomonadida
/ classification
Disease Vectors
/ classification
Fungi
/ classification
Host-Pathogen Interactions
/ genetics
Humans
Insecta
/ classification
Internet
Nematoda
/ classification
Phenotype
Phylogeny
User-Computer Interface
Virulence
Workflow
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
07 01 2022
07 01 2022
Historique:
accepted:
04
10
2021
revised:
21
09
2021
received:
15
09
2020
pubmed:
1
11
2021
medline:
25
2
2022
entrez:
31
10
2021
Statut:
ppublish
Résumé
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
Identifiants
pubmed: 34718728
pii: 6413610
doi: 10.1093/nar/gkab929
pmc: PMC8728164
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D898-D911Subventions
Organisme : NIAID NIH HHS
ID : 75N93019C00077
Pays : United States
Organisme : Wellcome Trust
ID : 218288/Z/19/Z
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 212929/Z/18/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
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