PHI-base: a new database for pathogen host interactions

A - Papers appearing in refereed journals

Winnenburg, R., Baldwin, T. K., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34 (1), pp. D459-D464.

AuthorsWinnenburg, R., Baldwin, T. K., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E.
Abstract

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/. 

KeywordsRRES175; 175_Genetics; 175_Bioinformatics; 175_Fungi; 175_Plant sciences
Year of Publication2006
JournalNucleic Acids Research
Journal citation34 (1), pp. D459-D464
Digital Object Identifier (DOI)doi:10.1093/nar/gkj047
Open accessPublished as ‘gold’ (paid) open access
Funder project or code513
505
Publication dates
Online01 Jan 2006
PublisherOxford University Press (OUP) Oxford
Copyright licenseCC BY

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