Skeletal Anatomy Jamboree

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Phenoscape Skeletal Anatomy Jamboree: April 9-10, 2010

A Phenoscape workshop (NSF grant BDI-0641025) hosted by the National Evolutionary Synthesis Center (NESCent)


Location and Date

Venue: National Evolutionary Synthesis Center (NESCent), Durham, NC (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.

Download the Vertebrate Anatomy Ontology

Download current release version in OBO or OWL format.

Download the version generated from discussion at the workshop here

Agenda

Friday, April 9, 2010

Morning

  • 8:30 SHUTTLE FROM HOTEL
  • 8:45 Coffee & pastries
  • 9:00-9:30 Welcomes and participant introductions (2-3 minute lightning talks)
  • 9:30-9:45 Paula Mabee: Introduction to workshop
  • 9:45-10:00 Brian Hall: Introduction to bone classification
  • 10:00-10:15 Melissa Haendel: Common Anatomy Reference Ontology and bone classification
  • 10:15 Coffee break
  • 10:45-11:00 Alex Diehl: Introduction to Cell Ontology and cross-products
  • 11:00-11:15 Wasila Dahdul: Introduction to ontologies and skeletal anatomy issues
  • 11:15-11:45 Group discussion on use cases
  • 11:45-12:00 Wrap up and devise breakout groups for afternoon
  • 12:00-12:15 Jim Balhoff: Introduction to Phenoscape Knowledgebase interfaces and mockups
  • 12:15 LUNCH

Afternoon User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)

  • 1:30 – 3:00 Break out groups
  • 3:00 Coffee break
  • 3:15-4:30 Reports from break out groups and ontology editing
  • 4:30 NESCent reception
  • 5:30 Shuttle back to hotel
  • 6:30 Shuttle from hotel to Carrboro Art Walk
  • 8:30 Dinner at Crook's Corner
  • 10:00 Shuttle back to hotel

Saturday, April 10, 2010

Morning

  • 8:30 SHUTTLE FROM HOTEL
  • 8:45 Coffee & pastries
  • 9:00-10:30 continue break out groups
  • 10:30 Coffee
  • 11:00-12:15 Reports from break out groups; ontology editing
  • 12:15 LUNCH

Afternoon User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)

  • 1:30-3:15 continue break out groups
  • 3:15 Coffee break
  • 3:45-5:00 Reports from break out groups; ontology editing
  • 5:00-5:30 Wrap up
  • 5:30 Van back to hotel
  • 6:15 Van from hotel to dinner Pop's

Sunday, April 11, 2010

  • Participants leave
  • 9-12 Phenoscape project meeting

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.(You should have gotten a copy of this by email; let us know if you need it)
  2. Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. (2010) The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology. doi:10.1093/sysbio/syq013
  3. Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007 Jul; 22(7) 345-50. doi:10.1016/j.tree.2007.03.013
  4. Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) CARO - The Common Anatomy Reference Ontology. In: Albert Burger, Duncan Davidson and Richard Baldock (Editors): Anatomy Ontologies for Bioinformatics: Principles and Practice. ISBN 978-1-84628-884-5.
  5. Hall, B. 2005. Bones and Cartilage: Developmental Skeletal Biology. Academic Press. 792 p. ISBN 978-0-12-319060-4.

Participants

Members of Phenoscape are in bold font.

Name Institution
Jim Balhoff Phenoscape and NESCent
David Blackburn Amphibian Anatomy Ontology (AmphibAnat) and University of Kansas
Wasila Dahdul Phenoscape, NESCent and University of South Dakota
Alexander Diehl Mouse Genome Informatics (MGI)
Melissa Haendel Oregon Health Sciences University
Brian Hall Department of Biology, Dalhousie University
John Lundberg Phenoscape and Department of Ichthyology, Academy of Natural Sciences, Philadelphia
Paula Mabee Phenoscape and Department of Biology, University of South Dakota
Peter Midford Phenoscape and NESCent
Martin Ringwald Mouse Genome Informatics (MGI)
Erik Segerdell Oregon Health Sciences University (representing Xenbase)
Ceri Van Slyke Zebrafish Information Network (ZFIN)
Matt Vickaryous Ontario Veterinary College, University of Guelph
Monte Westerfield Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon