Skeletal Anatomy Jamboree
**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
- 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
- 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)
- 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>
- 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>
- 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.
- 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 |
|——|—————————|