Evolutionary Biology and Ontologies 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 6, 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

July 6, 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

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) [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.

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.