Infectious Disease Ontology
Please Visit the Main IDO Website
The main IDO website is http://www.infectiousdiseaseontology.org.
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.
Medinfo 2010 Workshop
There will be an IDO workshop at the 13th World Congress on Medical and Health Informatics (Medinfo 2010). A separate wiki for this workshop can be found here: Infectious Disease Ontology Workshop - Medinfo 2010
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
Most current version of the ontology can be found here.
Meetings
2007
Infectious Disease Ontology Kick-off Workshop and Public Meeting at Cold Spring Harbor Laboratories
Past Meetings
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.
Training Workshop on Infectious Disease Ontology, Cold Spring Harbor Laboratories, NY: September 19-20, 2007
Public Meeting, Cold Spring Harbor Laboratories, NY: September 21, 2007
Report
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/
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
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
Workshop on the Ontology of Diseases, 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
To: "Smith, Barry" <phismith@buffalo.edu> Subject: save to
http://www.bioontology.org/wiki/index.php?title=Infectious_Disease_Onto logy&action=edit§ion=6
Past Meetings
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.
Training Workshop on Infectious Disease Ontology, Cold Spring Harbor Laboratories, NY: September 19-20, 2007
Public Meeting, Cold Spring Harbor Laboratories, NY: September 21, 2007
Report
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/
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
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
Workshop on the Ontology of Diseases, 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
- Sealife
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/
- Streaming video introduction to ontology by Barry Smith: http://ontology.buffalo.edu/smith/Ontology_Course.html
- 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