Evolutionary Biology and Ontologies

Introduction

This workshop will be held in conjunction with the Evolution 2008 meeting in Minneapolis, MN on June 20, 2008. It is organized under the auspices of the National Center for Biomedical Ontologies (NCBO) in collaboration with the National Evolutionary Synthesis Center (NESCent).

NESCent wiki

Workshop flyer

Venue

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.

Agenda

• 8:00 Registration

• 8:30-9:30 Tutorial: An Introduction to Ontology for Evolutionary Biology Slides

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

• 9:30-10:00 An Introduction to the PATO Phenotype Ontology Slides

Chris Mungall, NCBO / University of California, Berkeley

• 10:00-10:30 Morning Break

• 10:30-11:00 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

• 11:00-11:20 An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics

Paula Mabee, University of South Dakota

• 11:20-11:30 Phenote: Curation Software for Evolutionary Phenotypes Slides

James Balhoff, NESCent, Duke University

• 11:30-12:00 An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies

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

• 12:00-1:00 Lunch

• 1:00-1:30 Lightning Talks from Workshop Participants

• 1:30-2:00 Developing an Ontology for Amphibians using NLP Slides

Anne Maglia, University of Missouri-Rolla

• 2:00-2:30 Ontologies, Image Databases, and Evolutionary Biology Slides

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

• 2:30-2:45 Afternoon Break

• 2:45-3:15 An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits Slides

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

• 3:15-3:45 Names, Ranks, Clades, and Taxonomy Ontologies Slides

Peter Midford, Department of Ecology and Evolutionary Biology, University of Kansas

• 3:45-4:00 Synthesis

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

Background Reading

The OBO Foundry

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith b. (2008) CARO - The common anatomy reference ontology http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf 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. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 2007; 25 (11): 1251-1255.

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

Additional Resources

Michael Bada and Larry Hunter did an analysis of the glossary of terms for the book Being Alive (by Larry Hunter, forthcoming from MIT Press) found 189 terms that were not mappable to any OBO ontology. About half of these terms were related to evolution or population biology. The list of unmatched glossary terms is available and may be useful for ensuring the comprehensiveness of an evolutionary biology ontology.