Difference between revisions of "Infectious Disease Ontology"

Latest revision as of 06:53, 22 May 2015

More Information about IDO

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

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.

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

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

IDO Workshop, December 8-9, 2010

Further details are [here] Venue: to be determined

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-== New Email List ==
+== More Information about IDO ==
-Please subscribe to the Infectious Disease Ontology email.  Anyone can subscribe and anyone can send messages.  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/.  The email the list, write to ido@duke.edu.
+http://bioportal.bioontology.org/ontologies/IDO
-== Infectious Disease Ontology Kick-off Meeting ==
+== Beginnings of an Infectious Disease Ontology ==
-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].
+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.
-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 in pdf:  [[Image:IDO Draft.pdf]].  OBO edit and Protege OWL versions of the ontology are also available:
 * 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_9.21.07.obo
+* 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]]
-== Workshop Slides ==
+Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].
-* 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/
-== Recommended Background Reading ==
+== Past Meetings ==
-* For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/
-* For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image: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 [[Image: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
-== Downloads ==
+'''2007'''
-* 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
-== Meetings ==
+'''[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting]]''', Cold Spring Harbor Laboratories, NY, September 19-21, 2007
-September 19-20, 2007
+'''2008'''
-* [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]
-September 21, 2007
+'''[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]
-== Past Meetings ==
+'''2009'''
-November 6-7, 2006
+'''[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:
-** 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]
-== Links ==
+== Medinfo 2010 Workshop ==
+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]
+== IDO Workshop, December 8-9, 2010 ==
-* [http://diseaseontology.sourceforge.net/ The Disease Ontology]
-* [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]
+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]
+Venue: to be determined
-* [http://gemina.tigr.org Gemina Query Tool]
-* [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]
-* [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]