Skeletal Anatomy Jamboree

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Phenoscape Skeletal Anatomy Jamboree: April 9-10, 2010

A workshop hosted by the National Evolutionary Synthesis Center (NESCent)


Location and Date

Venue: National Evolutionary Synthesis Center (NESCent) (directions, also see information for visitors)

Date: April 9-10, 2010

Organizers: Paula Mabee, Wasila Dahdul

Introduction

The main focus of this meeting will be to re-evaluate the high-level skeletal system ontology hierarchy for fishes, particularly in relation to anatomy ontologies of other vertebrates. We will re-examine existing terms and definitions (cells, tissues, development, anatomical structures) for their applicability across vertebrates and redefine terms as necessary so that we leave with complete definitions. We will discuss how to represent of bone development within the structurally-defined hierarchy of the anatomy ontology. In addition, ontological issues such as multiple inheritance and cross-product definitions will be discussed although their solutions depend on the definitions we develop for the relevant terms.

Agenda

Friday, April 9, 2010

Morning

  • 8:30 SHUTTLE FROM HOTEL
  • 8:45 Coffee & pastries
  • 8:45-9:15 Welcomes and participant introductions
  • 9:15-9:45 Paula Mabee: Introduction to workshop
  • 9:45-10:15 Wasila Dahdul: Intro to ontologies and issues
  • 10:15-10:30 Brian Hall: Intro to bone classification
  • 10:30 Coffee break
  • 10:45-11:45 Group discussion on use cases
  • 11:45-12:15
  • 12:15 LUNCH

Afternoon -- breakout groups TBD

  • 1:30 – 2:00:
  • 2:00
  • 3:15 Coffee break
  • 3:30-4:15:
  • 4:15-5:00:
  • 5:00: Van back to hotel
  • 5:30-6:30: Drinks at hotel
  • 6:30 Van from hotel to dinner (whole group)

Saturday, April 10, 2010

Morning

  • 8:00 SHUTTLE FROM HOTEL
  • 8:15 Coffee & pastries
  • 8:30-9:30
  • 9:30-9:45
  • 9:45
  • 10:45 Coffee
  • 11:00-11:45 Phenoscape Knowledgebase usability testing concurrent with breakout groups
  • 11:45-12:15
  • 12:15 LUNCH

Afternoon

  • 1:30 – 2:00:
  • 2:00
  • 3:15 Coffee break
  • 3:30-4:15:
  • 4:15-5:00:
  • 5:00: Van back to hotel
  • 5:30-6:30: Drinks at hotel
  • 6:30 Van from hotel to dinner (whole group)

Sunday, April 11, 2010

  • Participants leave

Logistics

  • For long-distance participants, the hotel is the Millennium Hotel (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575)
  • For dining & entertainment, NESCent is right across from Ninth Street
  • For the venue, NESCent is in the historic Erwin Mills building (directions)

Reading

  1. Hall, B. K., and Witten, P. E. (2007). The Origin and Plasticity of Skeletal Tissues in Vertebrate Evolution and Development. In: Major Transitions in Vertebrate Evolution (Jason S. Anderson and Hans-Dieter Sues, eds). Festschrift for Dr. Robert L. Carroll. pp. 13-57. Indiana University Press, Bloomington, IN.
  2. Dahdul, W. M., J. G. Lundberg, P. E. Midford, J. P. Balhoff, H. Lapp, T. J. Vision, M. A. Haendel, M. Westerfield, and P. M. Mabee. 2010. The Teleost Anatomy Ontology: Anatomical representation for the genomics age. Systematic Biology, in press.
  3. Mabee P, Ashburner M, Cronk Q, Gkoutos G, Haendel M, et al. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution 22: 345-350.
  4. Haendel MA, Neuhaus F, Osumi-Sutherland DS, Mabee PM, Mejino JLV, et al. (2008) CARO–the common anatomy reference ontology. In: Burger A, Davidson D, Baldock R, editors. Anatomy Ontologies for Bioinformatics: Principles and Practice. London: Springer. pp. 327-349.
  5. Hall, B. 2005. Bones and Cartilage: Developmental Skeletal Biology. Academic Press. 792 p.

Participants

Members of Phenoscape are in bold font.

Name Institution
Jim Balhoff Phenoscape, NESCent
David Blackburn Amphibian Anatomy Ontology and University of Kansas
Wasila Dahdul Phenoscape, NESCent and Univesity of South Dakota
Andy Deans Hymenoptera Tree of Life and Department of Entomology, North Carolina State University
Betsy Dumont Department of Biology, Univerity of Massachusetts, Amherst
Eva Huala The Arabidopsis Information Resource
Hilmar Lapp Phenoscape and NESCent
Suzi Lewis Berkeley Bioinformatics and Ontology Project
Paula Mabee Phenoscape and Department of Biology, University of South Dakota
Anne Maglia Missouri University of Science and Technology
Austin Mast Florida State University
Peter Midford Phenoscape and Dept. of Ecology and Evolutionary Biology, University of Kansas
Cyndy Parr Smithsonian Institution and Encyclopedia of Life
Greg Riccardi College of Information, Florida State University
Paul Sereno University of Chicago
Arlin Stoltzfus Center for Advanced Research in Biotechnology, University of Maryland
Todd Vision Phenoscape, NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Peter Vize Department of Biology, University of Calgary
Monte Westerfield Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon