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.
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== Beginnings of an Infectious Disease Ontology ==
  
'''Recommended Background Reading'''
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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.ifomis.uni-saarland.de/projects/bfo/manual/: Comprehensive introduction to ontology in general and the Basic Formal Ontology specifically
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl
* Common Errors in OWL: http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj
* [[Relations_in_anatomical_ontologies_sa.pdf‎]]: explanation of the necessity of logic-based relations for automatic reasoning over ontologies
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* http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo
* [[Relations_in_Biomedical_Ontologies.pdf‎]]: Introduction to the Relations Ontology, describes the formulation of logic-based relations for OBO foundry ontologies
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*   A reference ontology for bioinformatics: the Foundational Model of Anatomy: http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf:
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* Ontology Development for Biological Systems: immunology: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913: Revisions to GO BP relevant to immunology
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'''Downloads'''
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Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]
* Download Protege OWL: 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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Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
  
September 19-20, 2007
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== Past Meetings ==
* [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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'''2007'''
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]
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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
  
'''Past Meetings'''
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'''2008'''
  
November 6-7, 2006
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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
* [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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'''2009'''
  
* [http://obofoundry.org The OBO Foundry]
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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://diseaseontology.sourceforge.net/ The Disease Ontology]
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Disease Main Page. http://www.bioontology.org/wiki/index.php/Disease:Main_Page
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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]]
  
I’ve added the most recent version of my Infectious Disease Ontology to the site, to the page.
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== IDO Workshop, December 8-9, 2010 ==
  
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Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]
 
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Venue: to be determined
The OBO file for my infectious disease ontology is also available on my FTP site at: ftp://ftp.tigr.org/pub/data/gemina/
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And it can be queried via a web page at the Gemina web page at: http://gemina.tigr.org
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I thought it might be useful for your students to view the work that’s been done in the field thus far.
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I was looking at your two day course and you mentioned that you would be putting together a disease ontology and
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looking at a Tuberculosis example.
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      I queried my Gemina site, to see how extensively we had covered this disease: we currently have 48 nodes for Tuberculosis
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      in our ontology.
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We haven’t curated Tuberculosis to any great extent yet, as our work has focused on diseases associated, thus far, with
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the category A-C pathogens. I hope that our site might be useful for your course.
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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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