PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

A - Papers appearing in refereed journals

Urban, M., Cuzick, A., Rutherford, K., Irvine, A. G., Pedro, H., Pant, R., Sadanadan, V., Khamari, L., Billal, S., Mohanty, Sagar and Hammond-Kosack, K. E. 2017. PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database. Nucleic Acids Research. 45 (D1), pp. D604-D610.

AuthorsUrban, M., Cuzick, A., Rutherford, K., Irvine, A. G., Pedro, H., Pant, R., Sadanadan, V., Khamari, L., Billal, S., Mohanty, Sagar and Hammond-Kosack, K. E.
Abstract

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed.

Year of Publication2017
JournalNucleic Acids Research
Journal citation45 (D1), pp. D604-D610
Digital Object Identifier (DOI)doi:10.1093/nar/gkw1089
PubMed ID27915230
PubMed Central IDPMC5210566
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
Copyright license
CC BY
Output statusPublished
Publication dates
Online03 Dec 2016
Publication process dates
Accepted27 Oct 2016
PublisherOxford University Press (OUP)
ISSN0305-1048

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