Difference between revisions of "Anatomy Ontology Workshop"

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== General Information ==
 
== General Information ==
  
The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. The workshop will take place on September 8-9, 2006 in Seattle.
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The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. The workshop will take place on September 8-9, 2006 in Seattle. Preliminary discussions are posted [http://www.bioontology.org/wiki/index.php/CARO:Main_Page here]. Listserv archives are available [http://listserv.buffalo.edu/archives/ontology-of-anatomy-list.html here].
 +
 
 +
== Participation ==
 +
 
 +
'''PLEASE NOTE THAT REGISTRATION IS CLOSED.'''
 +
 
 +
If you have any suggestions or questions about the workshop, please don't hesitate to contact [[User:Neuhaus| Fabian Neuhaus]].
  
 
== Aim of the workshop  ==  
 
== Aim of the workshop  ==  
At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy for a variety of organisms. Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species.
+
At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy ontologies for a variety of organisms. Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species.
  
 
The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies.  
 
The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies.  
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4. a method that allows automated reasoners to recognize homologous anatomical structures of different species.
 
4. a method that allows automated reasoners to recognize homologous anatomical structures of different species.
  
== Agenda ==
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In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. This common ontology will comprehend both top-level categories and a common set of relations to be used within anatomical ontologies; CARO will be embedded in set of principles for constructing anatomy ontologies for different organisms at different developmental stages. The discussion will be based on a pre-version of CARO.
In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. This common ontology will comprehend both top-level categories and a common set of relations to be used within anatomical ontologies; CARO will be embedded in set of principles for constructing anatomy ontologies for different organisms at different developmental stages. The discussion will be based on a pre-version of CARO.
+
 
 +
Issues to be addressed include:
 +
* The Range of CARO and its relation to species specific anatomies
 +
* Relations and development in CARO
 +
* The top level CARO universals
 +
* Concrete steps to implement CARO
 +
 
 +
Please also see the CARO wiki for discussion notes and other information.
 +
http://www.bioontology.org/wiki/index.php/CARO:Main_Page
  
The workshop will consist of four sessions (not necessarily in this order):
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== Agenda and Links to Meeting Minutes and Powerpoint Presentations ==
* The Range of CARO and it's Relation to Species Specific Anatomies
 
* Relations and Development in CARO
 
* The Top Level CARO Universals
 
* Concrete Steps to Implement CARO
 
  
== Participation ==
+
Minutes and Powerpoints posted on [[Shared_Materials#CARO_September_2006_meeting]]
For the usual practical reasons we want to keep the number of people attending small. This workshop is not open for participants who have only passing interest; we want to limit it to those who are in the trenches building these ontologies, since it sharpens the mind to have a tangible problem to be solved. Requests for participation are welcome. Please send a brief statement of your expertise to [[User:Neuhaus| Fabian Neuhaus]].
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Friday
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*9: 30am Session I:  Principles of Ontology Design ([http://ontology.buffalo.edu/medo/CARO_Smith.ppt Smith], Mungall)
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*2.00pm Session II: Current state of model organism anatomy ontologies (Haendel, Osumi-Sutherland)
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*Saturday
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*9.00am Session III: CARO a common anatomy reference ontology (Rosse)
 +
*2pm Session IV: Intelligent grouping of curations and use cases (Haendel, Osumi-Sutherland)
 +
*4pm Session V: Future Steps (Smith)
  
 
== Participants  ==
 
== Participants  ==
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 +
Stuart Aitken  -–  Artificial Intelligence Applications Institute, University of Edinburgh
 +
 
Michael Ashburner -– NCBO, University of Cambridge
 
Michael Ashburner -– NCBO, University of Cambridge
  
Carol Bean -–  National Institutes of Health
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Thomas Bittner -– Philosopy, University at Buffalo
 +
 
 +
Judith Blake -–  The Jackson Laboratory
  
 
Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh
 
Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh
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 +
Rex Chisholm -– Center for Genetic Medicine, Northwestern University
  
 
Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics  
 
Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics  
  
Melissa Haendel -– Zebrafish Information Network, University of Oregon
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Louis Goldberg -– Oral Biology, University at Buffalo
  
Thorsten Henrich -– European Molecular Biology Laboratory
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Peter Good -– National Human Genome Research Institute
  
Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory
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Melissa Haendel -– Zebrafish Information Network, University of Oregon
  
Fabian Neuhaus -– NCBO, University at Buffalo  
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Marc Halfon  -– Biochemistry, University at Buffalo
  
Onard Mejino -– Structural Informatics Group, University of Washington
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Terry Hayamizu  -– The Jackson Laboratory
  
Alan Rector -– Medical Informatics, University of Manchester
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David Hill -– The Jackson Laboratory
  
Martin Ringwald -– The Jackson Laboratory
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Ira Kalet -– Radiation Oncology, Biomedical Informatics, University of Washington
  
Cornelius Rosse -– Structural Informatics Group, University of Washington
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Raymond Lee  -– Biology, California Institute of Technology
  
Indra Neil Sarkar -– Invertebrate Zoology, American Museum of Natural History
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Jennifer Leopold  -– Computer Science, University of Missouri-Rolla
  
Barry Smith -– NCBO, University at Buffalo
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Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory
  
Ravensara Travillian -– Structural Informatics Group, University of Washington
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Kitsos Louis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas
  
Monte Westerfield -– Institute of Neuroscience, University of Oregon
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Paula Mabee -– Biology, University of South Dakota
  
== Venue ==
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Anne Maglia -– Biological Sciences, University of Missouri-Rolla
The event will be held at:
 
  
Silver Cloud Inns / Seattle-University Village
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Onard Mejino -– Structural Informatics Group, University of Washington
  
5036 25th Avenue NE
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Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory
  
Seattle, WA 98105
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Fabian Neuhaus -– NCBO, University at Buffalo
  
Phone: 206-526-5200
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Martin Ringwald -– The Jackson Laboratory
  
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Cornelius Rosse -– Structural Informatics Group, University of Washington
  
Silver Cloud Inns / Seattle-University Village is located just one mile from the University of Washington main campus, and two blocks from the upscale University Village shopping center. A complimentary continental breakfast is offered daily (6:30-9:30am M-F, 7:00-10:00am Sat/Sun). A fitness center, year round indoor pool and spa, and local area shuttle service is also available to Silver Cloud Inn guests.
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Indra Neil Sarkar -– Invertebrate Zoology, American Museum of Natural History
  
All guest rooms have complimentary high-speed internet access, microwaves, and refrigerators. We have negotiated a special guest room rate for Workshop attendees of $119 per night for a Standard King or Double Queen guest room. (For those Workshop participants wishing to extend their stay in Seattle, this rate will be offered for 3 days prior and/or after the conclusion of the event.) In order to receive this special rate, WORKSHOP PARTICIPANTS MUST MAKE ROOM RESERVATIONS BY AUGUST 24, 2006. After this date, all unreserved rooms within the NCBO block will be released for general sale at prevailing rates.
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Nigam Shah -– NCBO, Stanford Medical Informatics
  
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Barry Smith -– NCBO, University at Buffalo
  
To make room reservations online:
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David Osumi-Sutherland  -–  Genetics, University of Cambridge
  
1. Visit www.silvercloud.com
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Pantelis Topalis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas
  
2. Select "Reservations"
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Ravensara Travillian -– Structural Informatics Group, University of Washington
  
3. Select "Seattle-University District" under Properties
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Peter Vize  -– Biology, University of Calgary
  
4. Select "Group"
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Monte Westerfield -– Institute of Neuroscience, University of Oregon
 
 
5. Type in "Group Number": NCBO
 
 
 
6. Type in "Password": NCBO
 
 
 
7. Complete reservation
 
  
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== Venue ==
 +
The event will be held in Seattle, WA.
  
To make room reservations via telephone:
 
  
1. Call the hotel directly at 206-526-5200 or 800-205-6940
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==Related Links:==
  
2. Be sure to indicate that you are with the "NCBO Workshop" group (Group code: NCBO).
+
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Latest revision as of 07:02, 9 December 2010

General Information

The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. The workshop will take place on September 8-9, 2006 in Seattle. Preliminary discussions are posted here. Listserv archives are available here.

Participation

PLEASE NOTE THAT REGISTRATION IS CLOSED.

If you have any suggestions or questions about the workshop, please don't hesitate to contact Fabian Neuhaus.

Aim of the workshop

At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy ontologies for a variety of organisms. Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species.

The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies.

Its objectives are to develop:

1. a list of relations (especially part_of) used within anatomical anatomies, including definitions and rules for consistent use within anatomy ontologies ;

2. a list of major organizational units of biological organisms at all levels of granular partitions (e.g. biological macromolecule, cell, organ);

3. a representation of developmental stages of organisms; are anatomy and development two separate or one single integrated ontology? If separate what are the relations between them and how should they be applied;

4. a method that allows automated reasoners to recognize homologous anatomical structures of different species.

In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. This common ontology will comprehend both top-level categories and a common set of relations to be used within anatomical ontologies; CARO will be embedded in a set of principles for constructing anatomy ontologies for different organisms at different developmental stages. The discussion will be based on a pre-version of CARO.

Issues to be addressed include:

  • The Range of CARO and its relation to species specific anatomies
  • Relations and development in CARO
  • The top level CARO universals
  • Concrete steps to implement CARO

Please also see the CARO wiki for discussion notes and other information. http://www.bioontology.org/wiki/index.php/CARO:Main_Page

Agenda and Links to Meeting Minutes and Powerpoint Presentations

Minutes and Powerpoints posted on Shared_Materials#CARO_September_2006_meeting

Friday

  • 9: 30am Session I: Principles of Ontology Design (Smith, Mungall)
  • 2.00pm Session II: Current state of model organism anatomy ontologies (Haendel, Osumi-Sutherland)
  • Saturday
  • 9.00am Session III: CARO a common anatomy reference ontology (Rosse)
  • 2pm Session IV: Intelligent grouping of curations and use cases (Haendel, Osumi-Sutherland)
  • 4pm Session V: Future Steps (Smith)

Participants

Stuart Aitken -– Artificial Intelligence Applications Institute, University of Edinburgh

Michael Ashburner -– NCBO, University of Cambridge

Thomas Bittner -– Philosopy, University at Buffalo

Judith Blake -– The Jackson Laboratory

Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh

Rex Chisholm -– Center for Genetic Medicine, Northwestern University

Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics

Louis Goldberg -– Oral Biology, University at Buffalo

Peter Good -– National Human Genome Research Institute

Melissa Haendel -– Zebrafish Information Network, University of Oregon

Marc Halfon -– Biochemistry, University at Buffalo

Terry Hayamizu -– The Jackson Laboratory

David Hill -– The Jackson Laboratory

Ira Kalet -– Radiation Oncology, Biomedical Informatics, University of Washington

Raymond Lee -– Biology, California Institute of Technology

Jennifer Leopold -– Computer Science, University of Missouri-Rolla

Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory

Kitsos Louis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas

Paula Mabee -– Biology, University of South Dakota

Anne Maglia -– Biological Sciences, University of Missouri-Rolla

Onard Mejino -– Structural Informatics Group, University of Washington

Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory

Fabian Neuhaus -– NCBO, University at Buffalo

Martin Ringwald -– The Jackson Laboratory

Cornelius Rosse -– Structural Informatics Group, University of Washington

Indra Neil Sarkar -– Invertebrate Zoology, American Museum of Natural History

Nigam Shah -– NCBO, Stanford Medical Informatics

Barry Smith -– NCBO, University at Buffalo

David Osumi-Sutherland -– Genetics, University of Cambridge

Pantelis Topalis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas

Ravensara Travillian -– Structural Informatics Group, University of Washington

Peter Vize -– Biology, University of Calgary

Monte Westerfield -– Institute of Neuroscience, University of Oregon

Venue

The event will be held in Seattle, WA.


Related Links:

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