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 in pdf: File:IDO Draft.pdf. OBO edit and Protege OWL versions of the ontology are also available:

• http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl
• http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj
• http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.19.07.obo

Workshop Slides

• Morning Session 1: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt
• Morning Session 2: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt
• Afternoon and Evening Sessions:

http://ontology.buffalo.edu/bio/IDO/

Recommended Background Reading

• For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/
• For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see File:Relations in anatomical ontologies sa.pdf
• For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see File:Relations in Biomedical Ontologies.pdf
• For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf
• For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf
• For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913
• For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf
• For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf

Downloads

• Download the OBO-Edit ontology editor: http://oboedit.org/
• Download the Protege OWL ontology editor: 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

• TIGR's Gemina Project Infectious Disease Ontology
• TIGR's Gemina Project Infectious Disease Ontology Data
• Gemina Query Tool
• Mereotopology of Phagocytosis and Exocytosis
• Qualitative Simulation of Phagocytosis