Organization:Eukaryotic Pathogen Database
The Eukaryotic Pathogen, Vector & Host Informatics Resources, or VEuPathDB, is a database of genomic and other large-scale datasets related to various eukaryotic pathogens, as well as their vectors and hosts. VEuPathDB stores data related to its organisms of interest and provides tools for searching through and analyzing the data. It currently consists of 14 component data platforms, each dedicated to a certain research topic, in addition to the main VEuPathDB portal website. VEuPathDB includes:[1]
- Genomics resources covering eukaryotic protozoan parasites
- Host responses to parasite infection (HostDB)
- Orthologs (OrthoMCL)
- Clinical and epidemiological data (ClinEpiDB)
- Microbiome data (MicrobiomeDB)
History
VEuPathDB traces its origins to efforts in the early 2000s to organize genomic and related large-scale biological data for infectious disease research. Initial projects such as PlasmoDB (for Plasmodium spp.), CryptoDB (for Cryptosporidium), and ToxoDB (for Toxoplasma gondii) were developed as standalone databases focused on specific eukaryotic pathogens. These early component sites were integrated under the umbrella of ApiDB[2], established by the U.S. National Institute of Allergy and Infectious Diseases (NIAID) to support apicomplexan parasite research.
As the scope of the resource expanded to include a broader range of eukaryotic pathogens, the project was renamed EuPathDB to reflect its extended taxonomic coverage[3].
In parallel, VectorBase was developed to serve the invertebrate vector research community by providing similar genomic and functional datasets for disease vectors such as mosquitoes and ticks[4]. Both EuPathDB and VectorBase were funded as part of the NIH Bioinformatics Resource Centers (BRC) program, which began supporting pathogen and vector genomic resources in 2004.
In 2019, these two major resources were formally merged to create VEuPathDB, a unified bioinformatics platform integrating the strengths of EuPathDB and VectorBase into a single portal. This merger brought together data for eukaryotic pathogens, their invertebrate vectors, and relevant host organisms, supported by common infrastructure, analysis tools, and a shared web interface. The combined resource was designed to streamline data access and analysis for researchers studying infectious diseases and host-pathogen interactions[5].
Since the merger, VEuPathDB has continued to grow in scope and capability, incorporating thousands of curated datasets across diverse organisms and data types, expanding advanced search and visualization tools, and evolving its infrastructure to accommodate new analytic methods and user needs[6].
Functions
It is an integrated database covering the eukaryotic pathogens in several genera as well as hosts and vectors of these organisms. It enables the accessing of detailed genome information associated with these pathogens. VEuPathDB was formerly known as ApiDB and was the integrated resources for the apicomplexans covering the databases of associated pathogens, ToxoDB, PiroplasmDB and CryptoDB.[7]
VEuPathDB is noted for its sophisticated search strategy system and comprehensive gene pages, providing invaluable help to researchers.[8]
Component databases
Currently, VEuPathDB consists of 14 component data platforms, each with a particular focus, and a main portal site:[9]
- VEuPathDB (The main portal site)
- AmoebaDB (Pathogenic Amoeba)
- CryptoDB (Cryptosporidium species)
- FungiDB (Pathogenic fungi)
- GiardiaDB (Giardia species)
- MicrosporidiaDB (Microsporidia species)
- PiroplasmaDB (Pathogenic Piroplasmida)
- PlasmoDB (Plasmodium species)
- ToxoDB (Toxoplasma species)
- TrichDB (Trichomonas species)
- TriTrypDB (Kinetoplastida such as Leishmania and Trypanosoma species)
- HostDB (Host response to parasite infection)
- OrthoMCL (For orthologous protein sequences)
- ClinEpiDB (for data from clinical and epidemiological studies and trials)
- MicrobiomeDB (for microbiome data)
References
- ↑ "VEuPathDB". https://veupathdb.org/veupathdb/app/static-content/about.html.
- ↑ Aurrecoechea, Cristina; Heiges, Mark; Wang, Haiming; Wang, Zhiming; Fischer, Steve; Rhodes, Philippa; Miller, John; Kraemer, Eileen et al. (2007-01-01). "ApiDB: integrated resources for the apicomplexan bioinformatics resource center" (in en). Nucleic Acids Research 35 (suppl_1): D427–D430. doi:10.1093/nar/gkl880. ISSN 1362-4962. PMID 17098930. PMC 1669770. https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl880.
- ↑ Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan et al. (2016-11-29). "EuPathDB: the eukaryotic pathogen genomics database resource" (in en). Nucleic Acids Research 45 (D1): D581–D591. doi:10.1093/nar/gkw1105. ISSN 0305-1048. https://academic.oup.com/nar/article/45/D1/D581/2605823.
- ↑ Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M.; Maslen, Gareth; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Gesing, Sandra et al. (2015-01-28). "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases" (in en). Nucleic Acids Research 43 (D1): D707–D713. doi:10.1093/nar/gku1117. ISSN 1362-4962. PMID 25510499. PMC 4383932. https://academic.oup.com/nar/article/43/D1/D707/2437683.
- ↑ Amos, Beatrice; Aurrecoechea, Cristina; Barba, Matthieu; Barreto, Ana; Basenko, Evelina; Bażant, Wojciech; Belnap, Robert; Blevins, Ann S et al. (2022-01-07). "VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center" (in en). Nucleic Acids Research 50 (D1): D898–D911. doi:10.1093/nar/gkab929. ISSN 0305-1048. https://academic.oup.com/nar/article/50/D1/D898/6413610.
- ↑ Alvarez-Jarreta, Jorge; Amos, Beatrice; Aurrecoechea, Cristina; Bah, Saikou; Barba, Matthieu; Barreto, Ana; Basenko, Evelina Y; Belnap, Robert et al. (2024-01-05). "VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023" (in en). Nucleic Acids Research 52 (D1): D808–D816. doi:10.1093/nar/gkad1003. ISSN 0305-1048. PMID 37953350. PMC 10767879. https://academic.oup.com/nar/article/52/D1/D808/7416377.
- ↑ "ApiDB: integrated resources for the apicomplexan bioinformatics resource center". Nucleic Acids Res 35 (Database issue): D427-30. 2007. doi:10.1093/nar/gkl880. PMID 17098930.
- ↑ "EuPathDB: a portal to eukaryotic pathogen databases". Nucleic Acids Res 38 (Database issue): D415-9. 2010. doi:10.1093/nar/gkp941. PMID 19914931.
- ↑ "The Eukaryotic Pathogen genome resource". EuPathDB. http://www.eupathdb.org.
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