Rothamsted Research

where knowledge grows

PHI-base, the Pathogen-Host Interaction database is an open access internet resource which provides information on pathogenicity, virulence and effector genes from different pathogens, where the contribution of the genes to pathogenicity has been experimentally tested. In addition, at the request of the international community, negative results obtained from well designed and executed experiments have been included. PHI-base also provides information on commercially used drug targets and variant pathogen gene sequences which lead to drug-resistance / drug insensitivity. The phenomics information presented is based on manually curated information retrieved from the peer-reviewed scientific literature, and went on-line in 2005. PHI-base is a database which brings together genetic molecular and phenomic information and potentially has application to many different kinds of studies.

PHI-base version 4.0 (Sept 2015) provides functional information on 3944 genes from 262 pathogens tested on 165 hosts and their impact on 6473 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 FASTA or XML formats.

PHI-base is an invaluable 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

To date the use of PHI-base has been cited in over 140 peer-reviewed articles.

Improvements to PHI-base are currently supported by a BBSRC BBR award called PhytoPath: an Integrated resource for comparative phytopathogen genomics (BB/K020056/1).

We have linked in a gene centric manner the European Bioinformatics Institute's (EBI's) new Ensembl Genomes Browser interface for priority crop and model phytopathogenic species of fungi and oomycetes. Further information on this joint Phytopath project is available at

Science Team

Principle Investigator

Kim Hammond-Kosack

Team Members

Martin Urban
Alistair Irvine