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

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


* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms. 
Summary spreadsheet of rice disease: [https://docs.google.com/spreadsheets/d/1tJypvP9oQ2nb9m_HDj1Eqji2th6PbwGZrlo7lh-vD74/edit?usp=sharing PHI-Base_Plant_Diseases Google sheet]
* More information: 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:
Link to Spreadsheets on dropbox: [https://www.dropbox.com/s/wg5go0ce7vacd2n/PHI-Base_plants_LC_4-1-15.xlsx?dl=0 PHI-Base_plants_LC_4-1-15.xlsx]
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).
== Summary Discussions: ==
Follow up from Skype call 30th March, at 8.30am Pacific time:


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.
By email: from Alistair Irvine
Thank you for our interesting discussion today regarding the possibilities for collaboration to develop plant-related ontologies.
As discussed, we would be interested in establishing a controlled vocabulary for plant diseases. To facilitate this, I have set up a shared folder on ownCloud (our version of Dropbox), where we can share documents:


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.
https://rrescloud.rothamsted.ac.uk/public.php?service=files&t=be3a62e8d31c04d69f6cb89d3cd7cf83


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.
I have uploaded some documents here, including a copy of the spreadsheet that we use for curation, showing the various fields that we are currently capturing. I also uploaded a text file listing the disease names that are currently used in the PHI-base database. As you will see in the list, some of the same disease terms are named differently, and some are more specific than others - for example they may specify the disease host.


Kind Regards,
Regards,
Alistair.
 
----
 
By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:
Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden
Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden
* Interested in using ontologies to describing diseases in their database: 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).
* 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.


On 3/30/15 11:34 AM, Alistair Irvine wrote:
Thank you for our interesting discussion today regarding the possibilities for collaboration to develop plant-related ontologies.
As discussed, we would be interested in establishing a controlled vocabulary for plant diseases. To facilitate this, I have set up a shared folder on ownCloud (our version of Dropbox), where we can share documents:


https://rrescloud.rothamsted.ac.uk/public.php?service=files&t=be3a62e8d31c04d69f6cb89d3cd7cf83


http://www.phi-base.org/
I have uploaded some documents here, including a copy of the spreadsheet that we use for curation, showing the various fields that we are currently capturing. I also uploaded a text file listing the disease names that are currently used in the PHI-base database. As you will see in the list, some of the same disease terms are named differently, and some are more specific than others - for example they may specify the disease host.

Latest revision as of 23:01, 1 April 2015

Pathogen-Host Interaction Database (PHI-Base, http://www.phi-base.org/)

Goal: Annotates pathogen genes based on known interactions with host organisms

Summary spreadsheet of rice disease: PHI-Base_Plant_Diseases Google sheet

Link to Spreadsheets on dropbox: PHI-Base_plants_LC_4-1-15.xlsx


Summary Discussions:

Follow up from Skype call 30th March, at 8.30am Pacific time:

By email: from Alistair Irvine Thank you for our interesting discussion today regarding the possibilities for collaboration to develop plant-related ontologies. As discussed, we would be interested in establishing a controlled vocabulary for plant diseases. To facilitate this, I have set up a shared folder on ownCloud (our version of Dropbox), where we can share documents:

https://rrescloud.rothamsted.ac.uk/public.php?service=files&t=be3a62e8d31c04d69f6cb89d3cd7cf83

I have uploaded some documents here, including a copy of the spreadsheet that we use for curation, showing the various fields that we are currently capturing. I also uploaded a text file listing the disease names that are currently used in the PHI-base database. As you will see in the list, some of the same disease terms are named differently, and some are more specific than others - for example they may specify the disease host.

Regards, Alistair.

By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls: Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden

  • Interested in using ontologies to describing diseases in their database: 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).
  • 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.

On 3/30/15 11:34 AM, Alistair Irvine wrote: Thank you for our interesting discussion today regarding the possibilities for collaboration to develop plant-related ontologies. As discussed, we would be interested in establishing a controlled vocabulary for plant diseases. To facilitate this, I have set up a shared folder on ownCloud (our version of Dropbox), where we can share documents:

https://rrescloud.rothamsted.ac.uk/public.php?service=files&t=be3a62e8d31c04d69f6cb89d3cd7cf83

I have uploaded some documents here, including a copy of the spreadsheet that we use for curation, showing the various fields that we are currently capturing. I also uploaded a text file listing the disease names that are currently used in the PHI-base database. As you will see in the list, some of the same disease terms are named differently, and some are more specific than others - for example they may specify the disease host.

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