Difference between revisions of "Infectious Disease Ontology"

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== New Email List ==
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== More Information about IDO ==
  
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.
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http://bioportal.bioontology.org/ontologies/IDO
  
== Bare Beginnings of an Infectious Disease Ontology ==
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== 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.
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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.
 
* 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.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.pprj
* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo
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* 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]]
 
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) ==
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Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
  
The Infectious Disease Ontology Workshop (see link below under "Past Meetings") was intended to be 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).
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== Past Meetings ==
  
Workshop Slides
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'''2007'''
September 19, 2007
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* Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt
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* Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt
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* Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/
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Meeting Slides
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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
  
Recommended Background Reading
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'''2008'''
* 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 corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.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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Software Downloads
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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
* 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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== Past Meetings ==
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September 21, 2007
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'''2009'''
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]
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September 19-20, 2007
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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://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]
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November 6-7, 2006
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== Medinfo 2010 Workshop ==
* [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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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]]
** 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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== IDO Workshop, December 8-9, 2010 ==
  
* [http://obofoundry.org The OBO Foundry]
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Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]
* [http://diseaseontology.sourceforge.net/ The Disease Ontology]
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Venue: to be determined
* [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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* [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]
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* [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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* [http://www.phidias.us Pathogen-host interaction data integration and analysis system]
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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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