title: The Pathogen-Host Interactions database (PHI-base): additions and future developments.
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).
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK martin.urban@rothamsted.ac.uk.
authors.forename: Martin
authors.initials: M
authors.lastname: Urban
authors.affiliation: Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, Karnataka, India.
authors.forename: Rashmi
authors.initials: R
authors.lastname: Pant
authors.affiliation: Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, Karnataka, India.
authors.forename: Arathi
authors.initials: A
authors.lastname: Raghunath
authors.affiliation: Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
authors.forename: Alistair G
authors.initials: AG
authors.lastname: Irvine
authors.affiliation: European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Helder
authors.initials: H
authors.lastname: Pedro
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
authors.forename: Kim E
authors.initials: KE
authors.lastname: Hammond-Kosack
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000472:pathogenicity; D030541:Databases, Genetic; D005658:Fungi / Q000235:genetics / Q000472:pathogenicity; D054884:Host-Pathogen Interactions / Q000235:genetics*; D006801:Humans; D020407:Internet; D010641:Phenotype; D012984:Software; D014774:Virulence / Q000235:genetics; D018875:Vocabulary, Controlled