The Eukaryotic Pathogen Vector and Host Database, or VEuPathDB, is a database of genomics and experimental data related to various eukaryotic pathogens. It was established in 2006 under a

National Institutes of Health The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Service ...

program to create Bioinformatics Resource Centers to facilitate research on pathogens that may pose biodefense threats. 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 databases, each dedicated to a certain research topic. VEuPathDB includes: * Genomics resources covering eukaryotic protozoan parasites * Host responses to parasite infection (HostDB) * Orthologs (OrthoMCL) * Clinical study data (ClinEpiDB) * Microbiome data (MicrobiomeDB)

History

VEuPathDB was established under the

NIH The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Service ...

Bioinformatics Resource Centers program as ApiDB, a resource meant to cover

Apicomplexa The Apicomplexa (also called Apicomplexia; single: apicomplexan) are organisms of a large phylum of mainly parasitic alveolates. Most possess a unique form of organelle structure that comprises a type of non-photosynthetic plastid called an ap ...

n parasites. ApiDB originally consisted of component sites CryptoDB (for ''

Cryptosporidium ''Cryptosporidium'', sometimes called crypto, is an apicomplexan genus of alveolates which are parasitism, parasites that can cause a respiratory and gastrointestinal illness (cryptosporidiosis) that primarily involves watery diarrhea (inte ...

''), PlasmoDB (for ''

Plasmodium ''Plasmodium'' is a genus of unicellular eukaryotes that are obligate parasites of vertebrates and insects. The life cycles of ''Plasmodium'' species involve development in a Hematophagy, blood-feeding insect host (biology), host which then inj ...

''), and ToxoDB (for ''

Toxoplasma gondii ''Toxoplasma gondii'' () is a species of parasitic alveolate that causes toxoplasmosis. Found worldwide, ''T. gondii'' is capable of infecting virtually all warm-blooded animals, but members of the cat family (felidae) are the only known d ...

''). As ApiDB grew to focus on eukaryotic pathogens beyond Apicomplexans, the name was changed to EuPathDB to support its broadened scope. EuPathDB was the result of collaboration between many different parasitologists, including David Roos, Jessica Kissinger and Dyann Wirth. VEuPathDB provides public access to computational platforms and analysis tools enabling the collection, management, integration, and mining of genomic information and other large-scale datasets relevant to infectious disease pathogens, including their interaction with mammalian hosts and invertebrate vectors of disease.

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 A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

information associated with these pathogens. VEuPathDB was formerly known as ApiDB and was the integrated resources for the

apicomplexans The Apicomplexa (also called Apicomplexia; single: apicomplexan) are organisms of a large phylum of mainly parasitic alveolates. Most possess a unique form of organelle structure that comprises a type of non-photosynthetic plastid called an apico ...

covering the databases of associated pathogens, ToxoDB, PiroplasmDB and CryptoDB. VEuPathDB is noted for its sophisticated search strategy system and comprehensive gene pages, providing invaluable help to researchers.

Component databases

EuPathDB consists of 14 component databases, each with a particular focus: * AmoebaDB (Pathogenic amoeba) * CryptoDB (''Cryptosporidium'' species) * FungiDB (Pathogenic fungi) * GiardiaDB (''Giardia'' species) * MicrosporidiaDB (Microsporidia species) * PiroplasmaDB (Pathogenic

Piroplasmida Piroplasmida is an order of parasites in the phylum Apicomplexa. They divide by binary fission and as sporozoan parasites they possess sexual and asexual phases (sexual reproduction occurs in the tick gut). They include the tick parasites ''Ba ...

) * PlasmoDB (''Plasmodium'' species) * ToxoDB (''Toxoplasma gondii'') * TrichDB (''Trichomonas'' species) * TriTrypDB (Kinetoplastida such as ''Leishmania'' and ''Trypanosoma'' species) * HostDB (host response to parasite infection) * OrthoMCL (for orthologous protein sequences) * ClinEpiDB (for clinical study data) * MicrobiomeDB (for microbiome data)

References

{{Reflist Bioinformatics organizations Genome databases Pathogen genomics