PHI-base – a multi-species knowledge database to help protect crop yields and human health

6th Jan 2015

The Pathogen-Host Interactions database (PHI-base) catalogues 2872 genes and associated phenotypic information for economically important pathogens and pests.

Organisms that cause disease and epidemics affect crop yields as well as human and animal health. Molecular biology has advanced our understanding of the genes, proteins and metabolites of the hosts and the pathogens that are involved in the development of disease. Scientists at Rothamsted Research strategically supported by the BBSRC and in collaboration with other researchers globally have developed an Open Access internet resource that catalogues experimentally studied genes involved in host-pathogen interactions. A paper published at Nucleic Acids Research summarizes the improved content and how it can guide research approaches to pathogen control.

The updated PHI-base (version 3.6) provides functional information on 2875 genes from 160 pathogens tested on 110 hosts and their impact on 4102 interactions as well as on efficacy information of ~20 therapeutic drugs and the associated target sequences in the pathogen. PHI-base currently focusses on plant and human pathogenic organisms including fungi, protists and bacteria that have been studied for their role in the development of plant, animal and human disease.

Dr Martin Urban (Rothamsted Research) has been leading the technical side of the project, commented: “Over the last ten years we have been developing a comprehensive database that provides the scientific community with the necessary tools to advance their research in the areas of plant and human infectious diseases.”

The curated database integrates information from the relevant scientific literature, genome and protein databases and has expanded the taxonomic and species range of organisms covered. Major advances have also been made in the way that the information is presented in the database. All the information is free to download (

“Having received feedback from the community we have now further developed the database to contain more information, presented in a user-friendly way to enable use of the tool by researchers from a wide range of disciplines. Researchers can now use comparative genomics for the understanding and combating of disease in a wide range of organisms including crop plants, humans, farm animals, fish, insects and fungi.”

Professor Kim Hammond Kosack (Rothamsted Research) who is the project’s principal investigator commented: “PHI-base is an advanced phenomics tool to help researchers internationally to discover conserved genes in medically and agronomically important pathogens, and thus it may help with the identification of potential novel targets for intervention as well as for diagnostic purposes. Technological advances have revolutionized the way that data can be collected by biological scientists. Optimal utilization of this wealth of information requires the development of sophisticated but accessible and easy to use tools such as PHI-base. To date the use of PHI-base has been cited in over 100 peer-reviewed articles which indicates that it is highly useful and a reliable tool for researchers.”

PHI-base will celebrate its 10th anniversary in mid-2015. To mark this special occasion a one–day workshop is being organized for the early summer.

The Pathogen-Host Interactions database project is a National Capability strategically supported by the BBSRC (BB/J/004383/1). Improvements to PHI-base are currently supported by a BBSRC BBR award called PhytoPath: an Integrated resource for comparative phytopathogen genomics (BB/K020056/1), and were previously supported by the BBSRC BBR award (BB/I/001077/1). These projects also involve collaborators at the European Bioinformatics Institute in Cambridge, UK and the informatics company Molecular Connections based in Bangalore, India.

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