Difference between revisions of "Infectious Disease Ontology"
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== News == | == News == | ||
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In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here. | In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here. | ||
| − | + | == Recommended Background Reading == | |
* http://www.ifomis.uni-saarland.de/projects/bfo/manual/: Comprehensive introduction to ontology in general and the Basic Formal Ontology specifically | * http://www.ifomis.uni-saarland.de/projects/bfo/manual/: Comprehensive introduction to ontology in general and the Basic Formal Ontology specifically | ||
* Common Errors in OWL: http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf | * Common Errors in OWL: http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf | ||
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* Ontology Development for Biological Systems: immunology: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913: Revisions to GO BP relevant to immunology | * Ontology Development for Biological Systems: immunology: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913: Revisions to GO BP relevant to immunology | ||
| − | + | == Downloads == | |
* Download Protege OWL: http://protege.stanford.edu/download/download.html | * Download Protege OWL: http://protege.stanford.edu/download/download.html | ||
* Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under "Help" | * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under "Help" | ||
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* The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html | * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html | ||
| − | + | == Meetings == | |
September 19-20, 2007 | September 19-20, 2007 | ||
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* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics] | * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics] | ||
| − | + | == Past Meetings == | |
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November 6-7, 2006 | November 6-7, 2006 | ||
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Chris Mungall: DO and the OBO Foundry [[http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio] | Chris Mungall: DO and the OBO Foundry [[http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio] | ||
| − | + | == Links == | |
* [http://obofoundry.org The OBO Foundry] | * [http://obofoundry.org The OBO Foundry] | ||
Revision as of 09:47, 11 September 2007
News
The upcoming Infectious Disease Ontology Workshop (see link below under "Meetings") is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed here.
In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here.
Recommended Background Reading
- http://www.ifomis.uni-saarland.de/projects/bfo/manual/: Comprehensive introduction to ontology in general and the Basic Formal Ontology specifically
- Common Errors in OWL: http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf
- Relations_in_anatomical_ontologies_sa.pdf: explanation of the necessity of logic-based relations for automatic reasoning over ontologies
- Relations_in_Biomedical_Ontologies.pdf: Introduction to the Relations Ontology, describes the formulation of logic-based relations for OBO foundry ontologies
- A reference ontology for bioinformatics: the Foundational Model of Anatomy: http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf:
- Ontology Development for Biological Systems: immunology: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913: Revisions to GO BP relevant to immunology
Downloads
- Download Protege OWL: http://protege.stanford.edu/download/download.html
- Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under "Help"
- Download Pellet (a reasoner for OWL): http://pellet.owldl.com/
- The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html
Meetings
September 19-20, 2007
September 21, 2007
Past Meetings
November 6-7, 2006
- Workshop on Ontology of Diseases. See especially the links to presentations at this meeting:
Chris Mungall: DO and the OBO Foundry [Slides Audio