PHI-base- The Pathogen Host database

Correspondence by email: From Dr. Alistair Irvine to Ramona Walls > I am a developer of a database called the Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms. More information about PHI-base can be found from the website and from a recent paper published in Nucleic Acids Research (http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf).

> Obviously, one of the key aspects of any host-pathogen interaction is the disease that results from infection. I was hoping that the Plant Disease Ontology that you have been developing may be useful for describing diseases in our database. I read your interesting article from the 2012 Biomedical Ontology conference: > Walls, R., et al. (2012). A plant disease extension of the Infectious Disease Ontology. International Conference on Biomedical Ontology 2012. Graz, Austria. 897: 1-5.

> Currently, curation of diseases in PHI-base is performed through a > simple free text field. This causes predicable problems, as can be > since from the list of unique disease names that I extracted from > our database and have attached to this email. > > In your 2012 paper, you mention that researchers should contact you > before using IDOPlant, because it was still under development. I > wish to enquire about the current status of this project and if the > plant disease terms would be sufficient to describe the diseases in > our database (attached). > > I have downloaded the latest available Plant Disease Ontology OBO > file from > http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collabo > ra tors_ontology/plant_disease/plant_disease_ontology.obo?view=log, > but when I attempted to find diseases from our database I was not > successful. > > In addition to the disease, we do capture data regarding pathogen > species, host species, infected tissue, inducers, anti-infective > agent and more. Given the methodology in your paper, we could use > this information to define the disease. > > I would appreciate any advice you may be able to give regarding how > we may be able to use your ontology to describe diseases in PHI-base. > > Kind Regards, > > Dr. Alistair Irvine > > Postdoctoral Research Scientist > > Rothamsted Research > > Harpenden

http://www.phi-base.org/