Article |
PHI-base: a new database for pathogen host interactions
Biomathematics and Bioinformatics Division, Rothamsted Research Harpenden, AL5 2JQ, UK 1Wheat Pathogenesis Programme, Plant-Pathogen Interactions Division, Rothamsted Research Harpenden, AL5 2JQ, UK
*To whom correspondence should be addressed. Tel: +44 1582 763133; Fax: +44 1582 760089; Email: kim.hammond-kosack{at}bbsrc.ac.uk
Received August 15, 2005. Revised October 4, 2005. Accepted October 4, 2005.
To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogs 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene/transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, Enzyme Commission Numbers and so on), and provide links to other external data sources (e.g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at www4.rothamsted.bbsrc.ac.uk/phibase/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Soderlund Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes Brief Bioinform, November 1, 2009; 10(6): 654 - 663. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Winnenburg, M. Urban, A. Beacham, T. K. Baldwin, S. Holland, M. Lindeberg, H. Hansen, C. Rawlings, K. E. Hammond-Kosack, and J. Kohler PHI-base update: additions to the pathogen host interaction database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D572 - D576. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. C. Sexton and B. J. Howlett Parallels in Fungal Pathogenesis on Plant and Animal Hosts Eukaryot. Cell, December 1, 2006; 5(12): 1941 - 1949. [Full Text] [PDF]
|
|
|
|
 |
|
 J. Kohler, J. Baumbach, J. Taubert, M. Specht, A. Skusa, A. Ruegg, C. Rawlings, P. Verrier, and S. Philippi Graph-based analysis and visualization of experimental results with ONDEX Bioinformatics, June 1, 2006; 22(11): 1383 - 1390. [Abstract] [Full Text] [PDF]
|
|