The Pathogen-Host Interactions database (PHI-base): additions and future developments

A - Papers appearing in refereed journals

Urban, M., Pant, R., Raghunath, A., Irvine, A. G., Pedro, H. and Hammond-Kosack, K. E. 2015. The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Research. 43, pp. D645-D655.

AuthorsUrban, M., Pant, R., Raghunath, A., Irvine, A. G., Pedro, H. and Hammond-Kosack, K. E.
Abstract

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s).

Year of Publication2015
JournalNucleic Acids Research
Journal citation43, pp. D645-D655
Digital Object Identifier (DOI)doi:10.1093/nar/gku1165
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeWheat
Pathogen-Host Interactions Database: PHI Database [2012-2017]
[20:20 Wheat] Protecting yield potential of wheat
PhytoPath, an infrastructure for hundreds of plant pathogen genomes [2014-2017]
Publisher's version
Output statusPublished
Publication dates
Online20 Nov 2014
Publication process dates
Accepted30 Oct 2014
PublisherOxford University Press (OUP) Oxford
Oxford University Press (OUP)
Copyright licenseCC BY
ISSN0305-1048

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