PHI-base- The Pathogen Host database: Difference between revisions
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Summary Correspondence | =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 | ||
* 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. | ||
Revision as of 01:39, 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 of Correspondence:
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.