Difference between revisions of "Infectious Disease Ontology"

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== News ==
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== More Information about IDO ==
  
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 [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].
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http://bioportal.bioontology.org/ontologies/IDO
  
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:  [[Image:IDO Draft.pdf]]
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== Beginnings of an Infectious Disease Ontology ==
  
== Workshop Slides ==
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At the 2007 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.  More recent files and information about the email list can be found via the link above.
* Morning Session 1: http://www.duke.edu/~lgcowell/public_html/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo
  
== Recommended Background Reading ==
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Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]
* For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/
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* For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]
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* For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]
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* 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
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* 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
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* For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf
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* For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf
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== Downloads ==
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Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
* Download the OBO-Edit ontology editor: http://oboedit.org/
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* Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html
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* Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under "Help"
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* Download Pellet (a reasoner for OWL): http://pellet.owldl.com/
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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
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== Meetings ==
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== Past Meetings ==
  
September 19-20, 2007
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'''2007'''
* [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]
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September 21, 2007
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'''[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting]]''', Cold Spring Harbor Laboratories, NY, September 19-21, 2007
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]
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== Past Meetings ==
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'''2008'''
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'''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008 Infectious Disease Ontology Meeting]''', Buffalo, NY, September 16 - 17, 2008
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'''2009'''
  
November 6-7, 2006
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'''[https://www.vbi.vt.edu/component/option,com_events/Itemid,81/task,view_detail/agid,385/year,2010/month,3/day,24/ Presentation by Lindsay Cowell in Virginia Bioinformatics Institute]'''
* [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:
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** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]
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** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]
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**Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]
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** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]
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** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]
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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]
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== Links ==
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== Medinfo 2010 Workshop ==
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There will be an IDO workshop at the [http://www.medinfo2010.org/ 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]]
  
* [http://obofoundry.org The OBO Foundry]
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== IDO Workshop, December 8-9, 2010 ==
* [http://diseaseontology.sourceforge.net/ The Disease Ontology]
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* [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]
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Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]
* [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]
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Venue: to be determined
* [http://gemina.tigr.org Gemina Query Tool]
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* [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]
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* [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]
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Latest revision as of 06:53, 22 May 2015

Contents

[edit] More Information about IDO

http://bioportal.bioontology.org/ontologies/IDO

[edit] Beginnings of an Infectious Disease Ontology

At the 2007 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. More recent files and information about the email list can be found via the link above.

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.

[edit] Past Meetings

2007

Infectious Disease Ontology Kick-off Workshop and Public Meeting, Cold Spring Harbor Laboratories, NY, September 19-21, 2007

2008

Infectious Disease Ontology Meeting, Buffalo, NY, September 16 - 17, 2008

2009

Presentation by Lindsay Cowell in Virginia Bioinformatics Institute

[edit] 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

[edit] IDO Workshop, December 8-9, 2010

Further details are [here] Venue: to be determined

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