PHI-base

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The Pathogen-Host Host Interaction database (PHI-base) contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. The database was created and is maintained by researchers at Rothamsted Research and external collaborators since 2005.

Background[edit]

The Pathogen - Host Interaction database (http://www.phi-base.org) was developed to utilise effectively the growing number of verified genes that mediate an organism's ability to cause disease and / or to trigger host responses.

The web-accessible database catalogues experimentally verified pathogenicity, virulence and effector genes from fungal and Oomycete pathogens which infect animal, plant and fungal hosts. 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 strong 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 (fungicides).

Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene 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 structured description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes are annotated using controlled vocabularies (Gene Ontology terms, EC Numbers, etc.), and links to other external data sources (for example, NCBI taxonomy, EMBL and UniProt) are provided.

Current developments[edit]

The version 3.4 release (February 12th, 2013) of PHI-base provides information on 2420 genes from 107 pathogens and 92 hosts and their impact on 3138 interactions as well on efficacy information on ~20 drugs and the target sequences in the pathogen. PHI-base currently focusses on plant pathogenic and human pathogenic organisms including fungi, oomycetes and bacteria. The entire contents of the database can be downloaded in XML format.

PHI-base is a useful resource for many applications including:

› The discovery of conserved genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention

› Comparative genome analyses

› Annotation of newly sequenced pathogen genomes

› Functional interpretation of RNA sequencing and microarray experiments


Several specific improvements to PHI-base are currently supported. The PhytoPath project develops a bioinformatics resource that integrates genome-scale data from important plant pathogen species with the phenotypes captured in PHI-base. Using the Ensembl Genomes browser, PhytoPath provides access to complete genome assemblies and gene models of priority crop and model-fungal and oomycete phytopathogens.

References[edit]

Winnenburg, R., Urban, M., Beacham, A., Baldwin, T.K., Holland, S., Lindeberg, M., Hansen, H., Rawlings, C., Hammond-Kosack, K. and Köhler, J. 2008. PHI-base update: additions to the pathogen host interactions database. Nucleic Acids Research 36 (Database Issue): D572-6


Baldwin, T.K., Winnenburg, R., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity. Molecular Plant-Microbe Interactions 19(12):1451-62

Winnenburg, R., Baldwin, T.K., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34 (Database issue): D459-64

External links[edit]