Skeletal Anatomy Jamboree
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
- 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.
- 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.
- 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.
- 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.
- 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 |
