Difference between revisions of "Evolutionary Biology and Ontologies"

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(Draft Agenda)
(Draft Agenda)
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== Draft Agenda ==
 
== Draft Agenda ==
 
   
 
   
*9:00-10.00 '''''Tutorial: An Introduction to Ontology for Evolutionary Biology'''''
+
*9:00-10:00 '''''Tutorial: An Introduction to Ontology for Evolutionary Biology'''''
 
Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo
 
Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo
'''*10.00-10.30 Break'''
+
 
'''*10.30-11.00 ''An Introduction to the PATO Phenotype Ontology''''' - Chris Mungall, NCBO / University of California, Berkeley  
+
*10.00-10.30 Morning Break
'''*11:00-11:30 ''Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases''''' - Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR
+
 
'''*11:30-12:00 ''An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics''''' - Paula Mabee, University of South Dakota  
+
*10:30-11:00 '''''An Introduction to the PATO Phenotype Ontology'''''
*12:00-1:00 lunch
+
Chris Mungall, NCBO / University of California, Berkeley  
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: ''An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies''
+
 
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: ''Developing an Ontology for Amphibians using NLP''  
+
*11:00-11:30 '''''Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases'''''
*2:15-2:45 Coffee
+
Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR
*2:45-3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: ''Ontologies, Image Databases, and Evolutionary Biology''
+
 
*3.15-3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: ''An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits''
+
*11:30-12:00 '''''An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics'''''
*3:45-4:45 Roundtable & Discussion
+
Paula Mabee, University of South Dakota  
*4.45-5:00 Suzanna Lewis and Paula Mabee: ''Wrap-Up Session: Next Steps''
+
 
 +
*12:00-1:00 Lunch
 +
 
 +
*1:00-1:45 '''''An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies'''''
 +
Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR
 +
 
 +
*1:45-2:15 '''''Developing an Ontology for Amphibians using NLP'''''
 +
Anne Maglia, University of Missouri-Rolla
 +
 +
*2:15-2:45 Afternoon Break
 +
 
 +
*2:45-3:15 '''''Ontologies, Image Databases, and Evolutionary Biology'''''
 +
Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina
 +
 +
*3:15-3:45 '''''An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits'''''
 +
Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina
 +
 +
*3:45-4:45 '''''Roundtable & Discussion'''''
 +
 
 +
*4:45-5:00 '''''Wrap-Up Session: Next Steps'''''
 +
Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee:
  
 
== Background Reading ==
 
== Background Reading ==

Revision as of 11:33, 19 October 2007

Evolution2008-OntologyWorkshop.png

Introduction

This workshop will be held in conjunction with the Evolution 2008 meeting in Minneapolis, MN, 20 June 2008. It is organized under the auspices of the National Center for Biomedical Ontologies (NCBO) in collaboration with the National Evolutionary Synthesis Center (NESCent). Please disseminate widely using the URL for this page, or the workshop flyer.

Organizers
Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)
Focus
This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.
Goals
  1. Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
  2. Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
  3. Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?
Registration
Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

Draft Agenda

  • 9:00-10:00 Tutorial: An Introduction to Ontology for Evolutionary Biology

Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo

  • 10.00-10.30 Morning Break
  • 10:30-11:00 An Introduction to the PATO Phenotype Ontology

Chris Mungall, NCBO / University of California, Berkeley

  • 11:00-11:30 Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases

Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR

  • 11:30-12:00 An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics

Paula Mabee, University of South Dakota

  • 12:00-1:00 Lunch
  • 1:00-1:45 An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies

Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR

  • 1:45-2:15 Developing an Ontology for Amphibians using NLP

Anne Maglia, University of Missouri-Rolla

  • 2:15-2:45 Afternoon Break
  • 2:45-3:15 Ontologies, Image Databases, and Evolutionary Biology

Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina

  • 3:15-3:45 An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits

Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina

  • 3:45-4:45 Roundtable & Discussion
  • 4:45-5:00 Wrap-Up Session: Next Steps

Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee:

Background Reading

The OBO Foundry

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.

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