Difference between revisions of "Infectious Disease Ontology"

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== Please Visit the Main IDO Website ==
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== More Information about IDO ==
  
The main IDO website is http://www.infectiousdiseaseontology.org.
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http://bioportal.bioontology.org/ontologies/IDO
 
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== Email List ==
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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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== 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]]
+
  
 
== Beginnings of an Infectious Disease Ontology ==
 
== 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
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Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
 
Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
 
 
 
== Meetings ==
 
 
 
 
==2007==
 
[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting at Cold Spring Harbor Laboratories]]'''
 
 
 
[[IDO Kick-Off Meeting]]
 
  
 
== Past Meetings ==
 
== Past Meetings ==
  
'''Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007)'''
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'''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 [http://www.bwfund.org Burroughs Wellcome Fund].
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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
  
Training Workshop on Infectious Disease Ontology, Cold Spring Harbor Laboratories, NY: September 19-20, 2007
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'''2008'''
* [http://ontology.buffalo.edu/ido/2007_CSHL_Workshop.pdf Background]
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* http://ontology.buffalo.edu/ido/2007_CSHL_Workshop.pdf Program]
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Public Meeting, Cold Spring Harbor Laboratories, NY: September 21, 2007
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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://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]
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''Report''
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'''2009'''
  
*http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Infectious_Disease_Ontology_Meeting_Report.doc
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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]'''
  
''Slides''
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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]]
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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September 21, 2007
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*Topics in Infectious Disease Research
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**Stefan Kaufmann: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppt Global Threats Need Global Research Efforts: The Example of Tuberculosis]
+
**Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection
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*Ontologies and their Application to Infectious Disease
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**Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room
+
**Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]
+
**Lynn Schriml: The GEMINA Information Resource
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*Ontology and the Future of Infectious Disease Research (Panel Session)
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**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
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**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'''
+
 
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* [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:
+
** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]
+
** 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]
+
**Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]
+
** 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]
+
** 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]
+
** 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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+
 
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To: "Smith, Barry" <phismith@buffalo.edu>
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Subject: save to
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  http://www.bioontology.org/wiki/index.php?title=Infectious_Disease_Onto
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logy&action=edit&section=6
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+
== 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 [http://www.bwfund.org Burroughs Wellcome Fund].
+
 
+
Training Workshop on Infectious Disease Ontology, Cold Spring Harbor Laboratories, NY: September 19-20, 2007
+
* [http://ontology.buffalo.edu/ido/2007_CSHL_Workshop.pdf Background]
+
* http://ontology.buffalo.edu/ido/2007_CSHL_Workshop.pdf Program]
+
 
+
Public Meeting, Cold Spring Harbor Laboratories, NY: September 21, 2007
+
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]
+
 
+
''Report''
+
 
+
*http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Infectious_Disease_Ontology_Meeting_Report.doc
+
 
+
''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: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppt 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: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt 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'''
+
 
+
* [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:
+
** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]
+
** 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]
+
**Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]
+
** 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]
+
** 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]
+
** 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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* [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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* [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/phinfo Integrated pathogen-host interaction data in PHIDIAS]
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* [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]
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* [http://www.biotec.tu-dresden.de/sealife Sealife]
+
  
== Recommended Background Reading ==
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Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]
* For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/
+
Venue: to be determined
* Streaming video introduction to ontology by Barry Smith: http://ontology.buffalo.edu/smith/Ontology_Course.html
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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
+
* 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
+

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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