PHI-base- The Pathogen Host database: Difference between revisions
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=Pathogen-Host Interaction Database (PHI- | =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. | ||
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 of | |||
== 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. | |||
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By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls: | By email: Mon, Mar 23, 2015; Alistair Irvine to Ramona Walls: | ||
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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 | * 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. | ||
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
- More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.
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).
- 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
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.