NCBO Wiki - User contributions [en]

Infectious Disease Ontology

2007-09-22T19:49:35Z

Yongqunh:

== New Email List ==

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.

== Bare 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.
* 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

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) ==

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).

Workshop 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/

Meeting Slides

Recommended Background Reading
* 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

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

== Past Meetings ==

September 21, 2007
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]

September 19-20, 2007
* [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]

November 6-7, 2006
* [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 ==

* [http://obofoundry.org The OBO Foundry]
* [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]
* [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]
* [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]
* [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]
* [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]

Infectious Disease Ontology

2007-09-22T19:46:45Z

Yongqunh:

== New Email List ==

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.

== Bare 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.
* 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

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) ==

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).

Workshop 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/

Meeting Slides

Recommended Background Reading
* 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

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

== Past Meetings ==

September 21, 2007
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]

September 19-20, 2007
* [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]

November 6-7, 2006
* [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 ==

* [http://obofoundry.org The OBO Foundry]
* [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]
* [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]
* [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]
* [http://www.phidias.us PHIDIAS: Pathogen-host interaction data integration and analysis system]
* [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]

Infectious Disease Ontology

2007-09-22T19:44:36Z

Yongqunh:

== New Email List ==

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.

== Bare 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.
* 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

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) ==

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).

Workshop 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/

Meeting Slides

Recommended Background Reading
* 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

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

== Past Meetings ==

September 21, 2007
* [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]

September 19-20, 2007
* [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]

November 6-7, 2006
* [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 ==

* [http://obofoundry.org The OBO Foundry]
* [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]
* [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]
* [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]
* [http://www.phidias.us Pathogen-host interaction data integration and analysis system]