6 January 2015
Scientists at Rothamsted Research, which is strategically supported by BBSRC, in collaboration with other researchers globally have improved an Open Access internet resource that catalogues genes involved in host-pathogen interactions.
The Pathogen-Host Interactions database (PHI-base) catalogues 2872 genes and associated information for economically important pathogens and pests.
A paper published in Nucleic Acids Research summarises the improved content and how it can guide research approaches to pathogen control.
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.
The updated PHI-base (version 3.6) provides functional information on 2875 genes from 160 pathogens, tested on 110 hosts.
PHI-base currently focuses on plant and human pathogenic organisms including fungi and bacteria that have been studied for their role in the development of plant, animal and human disease.
Dr Martin Urban from Rothamsted Research has been leading the technical side of the project. He said: “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.
“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.”
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 at www.phi-base.org.
Professor Kim Hammond Kosack at Rothamsted Research, the project’s principal investigator, added: “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. PHI-base projects also involve collaborators at the European Bioinformatics Institute in Cambridge, UK and the informatics company Molecular Connections based in Bangalore, India.
Notes to editors
Publication: The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Research doi: 10.1093/nar/gku1165
About Rothamsted Research
We are the longest running agricultural research station in the world, providing cutting-edge science and innovation for nearly 170 years. Our mission is to deliver the knowledge and new practices to increase crop productivity and quality and to develop environmentally sustainable solutions for food and energy production. Our strength lies in the integrated, multidisciplinary approach to research in plant, insect and soil science.
Rothamsted Research is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC). In 2013-2014 Rothamsted Researched received a total of £32.9M from the BBSRC.