Data Jamboree 2

Linking Evolution to Genomics Using Phenotype Ontologies:
Second Morphology Data Jamboree

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

Location and Date

Venue: South Dakota Radisson Hotel, Rapid City (Sept. 27-29) Sylvan Lake Lodge, South Dakota (Sept. 29-Oct.1)

Date: September 27-October 1, 2008

Organizers: Paula Mabee, Monte Westerfield, Todd Vision, and Hilmar Lapp

Introduction

Purpose:

1. Evaluation of prototypes for web user interface
2. Character data entry by experts; introduce new curators to Phenote and data entry; test/enhance curation consistency; further refine curation interface
3. Project personnel meeting

Agenda

Draft at Data_Jamboree_2/Agenda for the program for each day.

Resources

For curators:

• Guide to Character Annotation
• Entering a taxon list
• Group exercise instructions
• Phenote User Guide (this also contains detailed instructions for downloading and running Phenote)
• Resources for curators

Logistics

• Radisson Hotel, Rapid City (Sept. 27-29)
• Sylvan Lake Lodge (Sept. 29-Oct.1)
• Buffalo Roundup (Sep 29)
• Travel agent: Marybeth Vlasman or Kristen Walker at AAA travel

Participants

Members of the project team are in bold font.

Name	Institution
Jim Balhoff	NESCent
Judith Blake	The Jackson Laboratory
Terry Grande	Loyola University, Chicago
Wasila Dahdul	University of South Dakota and NESCent
Jeff Engeman	University of South Dakota
Eric Hilton	Virginia Institute of Marine Science
Cartik Kothari	NESCent
Hilmar Lapp	NESCent
Suzanna Lewis	Berkeley Bioinformatics and Ontology Project
John Lundberg	Department of Ichthyology, Academy of Natural Sciences
Paula Mabee	University of South Dakota
Rick Mayden	St. Louis University
Peter Midford	Dept. of Ecology and Evolutionary Biology, University of Kansas
Mark Sabaj Pérez	Academy of Natural Sciences, Philadelphia
Todd Vision	NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Monte Westerfield	Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon

Papers for Annotation

for more information on the papers below see: http://spreadsheets.google.com/ccc?key=pTeXfTnVPxC-P1URVHbI4Qg&hl=en

• Terry Grande (Gonorynchiformes and Ostariophysi)
  • de Pinna, M. C. C.; Grande, T. (1993)
  • Grande, T. ; Poyato-Ariza, F J (1999)
  • Poyato-Ariza, F. J. (1996)

• Richard Mayden (Cypriniformes)
  • Mayden (1989)
  • Cavender & Coburn (1992)
  • Conway & Mayden (2007)

• Eric Hilton (Clupeiformes and Ostariophysi)
  • Chang, M-M; Maisey, J G (2003)
  • Arratia, G (1999)
  • Fink, S. V.; Fink, W. L. (1996) (review first pass by Wasila Dahdul)

• Mark Sabaj Perez (Siluriformes)
  • De Pinna (1993)
  • Mo (1991)
  • De Pinna (1996)

Background Reading

• We use the tag "phenoscape" on Connotea. Everyone is welcome to suggest references by using this tag.
• Relevant manuscripts by members of the project team:

1. 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
2. Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 2007 Jun 28. doi:10.1002/jez.b.21181
3. 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.