PHI-base- The Pathogen Host database - Revision history

Cooperl: /* Summary Discussions: */

2015-04-01T23:01:47Z

Summary Discussions:

← Older revision		Revision as of 23:01, 1 April 2015
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	* 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.		* 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.		* 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 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.		* 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.

Cooperl: /* Summary Discussions: */

2015-04-01T23:00:45Z

Summary Discussions:

← Older revision		Revision as of 23:00, 1 April 2015
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	Alistair.		Alistair.

	---		----

	By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:		By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:

Cooperl: /* Summary Discussions: */

2015-04-01T23:00:33Z

Summary Discussions:

← Older revision		Revision as of 23:00, 1 April 2015
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	Regards,		Regards,
	Alistair.		Alistair.

	---		---

	By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:		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

Cooperl at 23:00, 1 April 2015

2015-04-01T23:00:12Z

← Older revision		Revision as of 23:00, 1 April 2015
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	== Summary Discussions: ==		== 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:		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

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

2015-04-01T22:51:09Z

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

← Older revision		Revision as of 22:51, 1 April 2015
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	Summary spreadsheet of rice disease: [https://docs.google.com/spreadsheets/d/1tJypvP9oQ2nb9m_HDj1Eqji2th6PbwGZrlo7lh-vD74/edit?usp=sharing PHI-Base_Plant_Diseases Google sheet]		Summary spreadsheet of rice disease: [https://docs.google.com/spreadsheets/d/1tJypvP9oQ2nb9m_HDj1Eqji2th6PbwGZrlo7lh-vD74/edit?usp=sharing PHI-Base_Plant_Diseases Google sheet]

			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]


			== Summary Discussions: ==


	~~== Summary of Correspondence: ==~~

	By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:		By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls:

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

2015-04-01T22:48:42Z

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

← Older revision		Revision as of 22:48, 1 April 2015
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	Goal: Annotates pathogen genes based on known interactions with host organisms		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.		* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.

			Summary spreadsheet of rice disease: [https://docs.google.com/spreadsheets/d/1tJypvP9oQ2nb9m_HDj1Eqji2th6PbwGZrlo7lh-vD74/edit?usp=sharing PHI-Base_Plant_Diseases Google sheet]

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

2015-04-01T22:44:07Z

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

← Older revision		Revision as of 22:44, 1 April 2015
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	=Pathogen-Host Interaction Database (PHI-~~base~~, http://www.phi-base.org/)=		=Pathogen-Host Interaction Database (PHI-Base, http://www.phi-base.org/)=
	Goal: Annotates pathogen genes based on known interactions with host organisms		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.		* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.

Cooperl at 01:41, 1 April 2015

2015-04-01T01:41:03Z

← Older revision		Revision as of 01:41, 1 April 2015
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	Goal: Annotates pathogen genes based on known interactions with host organisms		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.		* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.



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	* 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.		* 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.

Cooperl at 01:39, 1 April 2015

2015-04-01T01:39:33Z

← Older revision		Revision as of 01:39, 1 April 2015
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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.




			== Summary of Correspondence: ==

			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

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

Cooperl at 01:35, 1 April 2015

2015-04-01T01:35:39Z

← Older revision		Revision as of 01:35, 1 April 2015
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	Summary Correspondence by email: Alistair Irvine to Ramona Walls:		Summary Correspondence by email: Alistair Irvine to Ramona Walls:
			Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden

	* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms.		* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which 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.		* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.
			* 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.
	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~~:		* 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.
	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 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.		* 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.		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/~~