The Eukaryotic Pathgen Database, or EuPathDB, is a database of bioinformatic and experimental data related to a variety of eukaryotic pathogens. It was established in 2006 under a National Institutes of Health program to create
Bioinformatics Resource Centers The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID (the National Institute of Allergy and Infectious Diseases.)NIH Bioinformatics Resource Centers program as ApiDB, a resource meant to cover Apicomplexan parasites. ApiDB originally consisted of component sites CryptoDB (for ''
Cryptosporidium
''Cryptosporidium'', sometimes informally called crypto, is a genus of apicomplexan parasitic alveolates that can cause a respiratory and gastrointestinal illness (cryptosporidiosis) that primarily involves watery diarrhea (intestinal cryptosp ...
''), PlasmoDB (for '' Plasmodium''), and ToxoDB (for '' Toxoplasma gondii''). 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
Jessica Kissinger is a Distinguished Research Professor at the Franklin College of Arts and Sciences, University of Georgia and director of the Institute of Bioinformatics. Her research focus is on the evolution, assembly and data curation of proto ...
and
Dyann Wirth
Dyann F. Wirth (born Dyann Lynn Fergus, January 31, 1951, Racine, Wisconsin) is an American immunologist. She is currently the Richard Pearson Strong Professor of Infectious Diseases at Harvard T.H. Chan School of Public Health.
Wirth is one of ...
.
Functions
It is an integrated database covering the eukaryotic pathogens in several genera. It enables the accessing of detailed genome information associated with these pathogens. EuPathDB was formerly known as ApiDB and was the integrated resources for the
apicomplexans
The Apicomplexa (also called Apicomplexia) are a large phylum of parasitic alveolates. Most of them possess a unique form of organelle that comprises a type of non-photosynthetic plastid called an apicoplast, and an apical complex structure. T ...
covering the databases of associated pathogens, ToxoDB, PiroplasmDB and CryptoDB.
Presently EuPathDB covers 11 databases, the latest addition being that of Piroplasma which supports '' Babesia'' and ''
Theileria
''Theileria'' is a genus of parasites that belongs to the phylum Apicomplexa, and is closely related to ''Plasmodium''. Two ''Theileria'' species, ''T. annulata'' and ''T. parva'', are important cattle parasites. ''T. annulata'' causes tropical ...
''. This BRC is one of five centres being funded to provide
support to research bodies. EuPath supports the investigation of eukaryotic pathogens, and the other four centres support the investigation of other disease pathogens. It has developed a sophisticated search system providing invaluable help to researchers.
Component databases
EuPathDB consists of 14 component databases, each with a particular focus:
*
AmoebaDB
AmoebaDB is a functional genomics
Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic ...
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 PlasmoDB is a ''biological database'' for the genus ''Plasmodium''. The database is a member of the ''EuPathDB'' project. The database contains extensive ''genome'', ''proteome'' and ''metabolome'' information relating to malaria parasites.
See als ...
(''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)