PHI-base- The Pathogen Host database: Difference between revisions

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Correspondence by email:  
Summary Correspondence by email: Alistair Irvine to Ramona Walls:
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:
* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms.
> 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.
* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.


> Currently, curation of diseases in PHI-base is performed through a
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:
> simple free text field. This causes predicable problems, as can be
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.
> since from the list of unique disease names that I extracted from
 
> our database and have attached to this email.
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
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).
> before using IDOPlant, because it was still under development. I
 
> wish to enquire about the current status of this project and if the
I have downloaded the latest available Plant Disease Ontology OBO file from http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/plant_disease_ontology.obo?view=log, but when I attempted to find diseases from our database I was not successful.
> plant disease terms would be sufficient to describe the diseases in
 
> our database (attached).
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 have downloaded the latest available Plant Disease Ontology OBO
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.
> file from
 
> http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collabo
Kind Regards,
> ra tors_ontology/plant_disease/plant_disease_ontology.obo?view=log,
Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden
> 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




Revision as of 01:32, 1 April 2015

Summary Correspondence by email: Alistair Irvine to Ramona Walls:

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/collaborators_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/

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