Difference between revisions of "Evolutionary Biology and Ontologies 2009"

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This workshop will be held in conjunction with the Annual Meeting of the
 
This workshop will be held in conjunction with the Annual Meeting of the
Society for Integrative and Comparative Biology (SICB) in Boston, MA on January 6,
+
Society for Integrative and Comparative Biology ([http://www.sicb.org/meetings/2009/index.php3 SICB]) in Boston, MA on January 5, 2009.  It is cosponsored by the National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]) and the National Center for Biomedical Ontologies ([http://bioontology.org NCBO]).
2009.  It is cosponsored by the [http://www.nescent.org National Evolutionary Synthesis Center
+
(NESCent)] and the [[http://bioontologies.org National Center for Biomedical Ontologies (NCBO)].
+
  
 
'''Organizers'''
 
'''Organizers'''
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'''Agenda'''
 
'''Agenda'''
  
July 6, 2009
+
January 5, 2009
  
 
8:00: Todd Vision (University of North Carolina, NESCent) - Introduction
 
8:00: Todd Vision (University of North Carolina, NESCent) - Introduction
  
8:05: Barry Smith (University of Buffalo, NCBO) - Introduction to ontologies
+
8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists
  
 
8:35: Monte Westerfield (Zebrafish Information Service, University of
 
8:35: Monte Westerfield (Zebrafish Information Service, University of
Oregon) - Comparison of phenotypes across model organisms
+
Oregon) - Linking animal models and human diseases
  
9:00: Paula Mabee (University of South Dakota) - Phenoscape: extending model
+
9:00: Paula Mabee (University of South Dakota) - [http://phenoscape.org Phenoscape]: extending model organism ontologies for devo-studies of evolutionary phenotypes
organism ontologies for devo-studies of evolutionary phenotypes
+
  
 
9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
 
9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
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behavior using ontologies
 
behavior using ontologies
  
11:20: Anne Maglia (Missouri): Developing an amphibian ontology
+
11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology
 +
 
 +
11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up
 +
 
 +
'''Download presentations'''
 +
 
 +
The Powerpoint files for each presentation is available from [http://phenoscape.org/wiki/Training_and_Workshops this page on the Phenoscape wiki]
  
11:50: Wrap-up
 
  
 
'''Background Reading'''
 
'''Background Reading'''
Line 66: Line 68:
 
morphological ontology. ''Systematic Biology'', 56, 283-94.
 
morphological ontology. ''Systematic Biology'', 56, 283-94.
  
Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated
+
Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration].  ''Nature Biotechnology'', 25, 1251-1255.
evolution of ontologies to support biomedical data integration].  ''Nature
+
Biotechnology'', 25, 1251-1255.
+
  
Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies. ''Genome Biology'', 6 (5), R46.
+
Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies]. ''Genome Biology'', 6 (5), R46.

Latest revision as of 09:09, 6 January 2009

This workshop will be held in conjunction with the Annual Meeting of the Society for Integrative and Comparative Biology (SICB) in Boston, MA on January 5, 2009. It is cosponsored by the National Evolutionary Synthesis Center (NESCent) and the National Center for Biomedical Ontologies (NCBO).

Organizers Paula Mabee, Barry Smith, Todd Vision, Monte Westerfield.

Goals The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.

Registration Registration is open to attendees of the SICB 2009 conference at no additional cost.

Agenda

January 5, 2009

8:00: Todd Vision (University of North Carolina, NESCent) - Introduction

8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists

8:35: Monte Westerfield (Zebrafish Information Service, University of Oregon) - Linking animal models and human diseases

9:00: Paula Mabee (University of South Dakota) - Phenoscape: extending model organism ontologies for devo-studies of evolutionary phenotypes

9:20: Wasila Dahdul (University of South Dakota; National Evolutionary Synthesis Center): The promises and pitfalls of multi-species anatomy ontologies

9:40: James Balhoff (National Evolutionary Synthesis Center): Software and database resources for curation and management of evolutionary phenotypes

10:00: BREAK

10:20: Andy Deans (North Carolina State University): Developing a Hymenopteran ontology

10:50: Peter Midford (University of Kansas): Comparative Analysis of behavior using ontologies

11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology

11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up

Download presentations

The Powerpoint files for each presentation is available from this page on the Phenoscape wiki


Background Reading

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith B (2008) CARO - The common anatomy reference ontology In: Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution, 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology for amphibians. Pacific Symposium on Biocomputing, 12: 367-378.

Midford PE (2004) Ontologies for behavior. Bioinformatics, 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC (2007) Text linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology, 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. (2007) The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25, 1251-1255.

Smith B, Ceusters W, Klagges B, et al. (2005) Relations in biomedical ontologies. Genome Biology, 6 (5), R46.

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