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. 2008 Jan;36(Database issue):D572-6.
doi: 10.1093/nar/gkm858. Epub 2007 Oct 16.

PHI-base Update: Additions to the Pathogen Host Interaction Database

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Free PMC article

PHI-base Update: Additions to the Pathogen Host Interaction Database

Rainer Winnenburg et al. Nucleic Acids Res. .
Free PMC article

Abstract

The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/.

Figures

Figure 1.
Figure 1.
Predicted virulence genes for the newly sequenced fish pathogen V. salmonicida (Vs). Vs genes are displayed as circles, PHI-base genes are displayed as rectangles and are colour coded to indicate type. The arcs between the genes represent sequence–homology relationships. The visualization tool has placed ∼50 putative Vs virulence genes in V. salmonicida into distinct clusters of PHI-base entries.

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