Infectious Disease Ontology

New Email List

Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.

Bare Beginnings of an Infectious Disease Ontology

At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.

• 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_10.08.07.obo

Accessible data to test the ontology, existing ontologies of related interest can be found here: Toolbox

Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007)

The Infectious Disease Ontology Workshop and Meeting (see link below under "Past Meetings") were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the Burroughs Wellcome Fund.

Workshop Slides

September 19, 2007

• Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt
• Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt
• Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/

Meeting Slides

September 21, 2007

• Topics in Infectious Disease Research
  • Stefan Kaufmann: Global Threats Need Global Research Efforts: The Example of Tuberculosis
  • Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection
• Ontologies and their Application to Infectious Disease
  • Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room
  • Michael Ashburner: Ontologies for Biomedicine: The GO Experience
  • Lynn Schriml: The GEMINA Information Resource
• Ontology and the Future of Infectious Disease Research (Panel Session)
  • Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt
  • Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt
  • Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt

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

Software 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

Past Meetings

September 21, 2007

• Infectious Disease: A Challenge for Biomedical Informatics

September 19-20, 2007

• Training Workshop on Infectious Disease Ontology

November 6-7, 2006

• Workshop on Ontology of Diseases. 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
• Integrated pathogen-host interaction data in PHIDIAS
• VIOLIN: University of Michigan Vaccine Database