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Nucleic Acids Research Advance Access published online on October 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm858
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PHI-base update: additions to the pathogen–host interaction database

Rainer Winnenburg1, Martin Urban2, Andrew Beacham2, Thomas K. Baldwin2, Sabrina Holland3, Magdalen Lindeberg4, Hilde Hansen5, Christopher Rawlings1, Kim E. Hammond-Kosack2,* and Jacob Köhler1,5

1Department of Biomathematics and Bioinformatics, 2Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, AL5 2JQ, UK, 3Institute of Zoology, Johannes Gutenberg-University, Becherweg 9-11, D-55099 Mainz, Germany, 4Department of Plant Pathology, Plant Science Building, Cornell University, Ithaca, NY 14853, USA and 5Protein Research Group, Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway

* To whom correspondence should be addressed. Tel: 0044 1582 763133; Fax: 0044 1582 760981; Email: kim.hammond-kosack{at}bbsrc.ac.uk

Received September 11, 2007. Accepted September 26, 2007.

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/.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.


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