Infectious Disease Ontology

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

• Training Workshop on Infectious Disease Ontology

September 21, 2007

• Infectious Disease: A Challenge for Biomedical Informatics

Past Meetings

November 6-7, 2006

• Workshop on Ontology of Diseases. See especially the links to presentations at this meeting:
  • Kent Spackman: SNOMED CT Slides
  • Barry Smith: What a Disease Ontology is For Slides Audio
  • Neil Williams: The Ontology of Powers, Dispositions and Tendencies Slides
  • Louis J. Goldberg: Networks and the Ontology of Disease Slides Audio
  • Werner Ceusters: The Ontology of Diagnosis: Slides Audio

Chris Mungall: DO and the OBO Foundry [Slides Audio

Links

• The OBO Foundry
• The Disease Ontology

Disease Main Page. http://www.bioontology.org/wiki/index.php/Disease:Main_Page

I’ve added the most recent version of my Infectious Disease Ontology to the site, to the page.

The OBO file for my infectious disease ontology is also available on my FTP site at: ftp://ftp.tigr.org/pub/data/gemina/

And it can be queried via a web page at the Gemina web page at: http://gemina.tigr.org

I thought it might be useful for your students to view the work that’s been done in the field thus far.

I was looking at your two day course and you mentioned that you would be putting together a disease ontology and

looking at a Tuberculosis example.

      I queried my Gemina site, to see how extensively we had covered this disease: we currently have 48 nodes for Tuberculosis

      in our ontology.

We haven’t curated Tuberculosis to any great extent yet, as our work has focused on diseases associated, thus far, with 

the category A-C pathogens. I hope that our site might be useful for your course.