Eukaryotic Pathogen Database

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 to facilitate research on pathogens that may pose biodefense threats. EuPathDB 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. EuPathDB includes:

  • Genomics resources covering eukaryotic protozoan parasites
  • Host responses to parasite infection (HostDB)
  • Orthologs (OrthoMCL)
  • Clinical study data (ClinEpiDB)
  • Microbiome data (MicrobiomeDB)

History

EuPathDB was established under the NIH Bioinformatics Resource Centers program as ApiDB, a resource meant to cover Apicomplexan parasites.[1] ApiDB originally consisted of component sites CryptoDB (for Cryptosporidium), PlasmoDB (for Plasmodium), and ToxoDB (for Toxoplasma gondii).[2] As ApiDB grew to focus on eukaryotic pathogens beyond Apicomplexans, the name was changed to EuPathDB to support its broadened scope.[3] EuPathDB was the result of collaboration between many different parasitologists, including David Roos, Jessica Kissinger and Dyann Wirth.[4][5]

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 covering the databases of associated pathogens, ToxoDB, PiroplasmDB and CryptoDB.[2]

Presently EuPathDB covers 11 databases, the latest addition being that of Piroplasma which supports Babesia and Theileria. 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.[6] It has developed a sophisticated search system providing invaluable help to researchers.[3]

Component databases

EuPathDB consists of 14 component databases, each with a particular focus:[7]

  • AmoebaDB (Pathogenic amoeba)
  • CryptoDB (Cryptosporidium species)
  • FungiDB (Pathogenic fungi)
  • GiardiaDB (Giardia species)
  • MicrosporidiaDB (Microsporidia species)
  • PiroplasmaDB (Pathogenic Piroplasmida)
  • 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)
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gollark: You need to deal with too many goods in too many locations with weird stuff like economies and diseconomies of scale.
gollark: Also, it has incentives problems, as well as information flow problems.
gollark: As I said, central planning is computationally intractable.
gollark: What? We DON'T use a centrally planned economy in capitalism. It would be bad.

References
  1. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Francsco VD. "National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics". Cite journal requires |journal= (help)
  2. Aurrecoechea C, Heiges M, Wang H, Wang Z, Fischer S, Rhodes P, Miller J, Kraemer E, Stoeckert CJ Jr, Roos DS, Kissinger JC (2007). "ApiDB: integrated resources for the apicomplexan bioinformatics resource center". Nucleic Acids Res. 35: D427-30. doi:10.1093/nar/gkl880. PMC 1669770. PMID 17098930.
  3. Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H (2010). "EuPathDB: a portal to eukaryotic pathogen databases". Nucleic Acids Res. 38: D415-9. doi:10.1093/nar/gkp941. PMC 2808945. PMID 19914931.
  4. "Parasitologist, Reprogrammed: A Profile of David Roos". The Scientist Magazine®. Retrieved 2019-08-02.
  5. "EuPathDB : About All". eupathdb.org. Retrieved 2019-08-02.
  6. Aurrecoechea C, Barreto A, et al. (2013). "EuPathDB:the eukaryotic pathogen database". Nucleic Acids Research. 41: D684-91. doi:10.1093/nar/gks1113. PMC 3531183. PMID 23175615.
  7. "The Eukaryotic Pathogen genome resource". EuPathDB. Retrieved 2013-11-11.
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