Needs Analysis Workshop

Linking Evolution to Genomics Using Phenotype Ontologies:
Needs Analysis Workshop

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: September 17-18, 2007

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

Introduction

This workshop brings together scientists from the fields of morphology, development, evolution, genetics, and ichthyology to define what informatic tools need to exist in order to enable synthetic research that takes full advantage of the accumulated data in each of these fields. The workshop organizers are funded by NSF to develop a system that provides web-based access to integrated evolutionary, anatomical, developmental, and genetics data in the Ostariophysii, and to make the software tools a community resource that can be more broadly applied. Thus, a major goal of the workshop is to identify driving biological research questions that take advantage of these data to push the limits of what is currently possible, and to identify what informatic tools are needed in order to answer those questions. These will, in turn, be distilled to Use Cases that drive the software development activities at NESCent.

Final Report

For a summary of the outcomes of this report, see here.

Agenda

Monday, September 17

• 8.30am NESCent introduction (K. Smith, J. Sturkey)
• 8.45am Introduction to Workshop
  • Participant introductions (10mins)
  • Linking Evolution to Genomics: Motivation, Approach, Project Goals (P. Mabee, 15mins)
  • Uncovering gene function through mutant phenotypes in zebrafish, a model organism (M. Westerfield, 15mins)
  • Managing of and computing with phenotypes, evolutionary change, and genetics: Informatics challenges (T. Vision, 15mins)
• 9.40am Opportunities and research challenges
  • Chalk talks (5mins each)
  • Goals of the workshop (H. Lapp)
• 10.25am Coffee break
• 10.45am Break-out groups
  • Break-out group 1: Developmental genetics of morphology
  • Break-out group 2: Evolution of morphology
• 12.00pm Lunch break
• 1.15pm Continuation of break-out groups, with some participants rotating to different groups
• 2.45pm Coffee break
• 3.15pm Report-out from break-out groups, and large group discussion (40mins per group)
• 4.40pm Discussion of topics for second day
• 5:00pm shuttle to Millennium Hotel
• 6:00pm shuttle from Millennium to Kanki restaurant (Charlene's Safe Ride, not the Millennium shuttle), 3504 Mt. Moriah Road, Durham. Reservations are for 6:30pm.

Tuesday, September 18

• 9.00am Break-out groups (new composition, topics arisen from previous day)
  1. Semantics
  2. Correlation of traits
  3. Phylogeny
• 10.15am Coffee break
• 10.30am Report-out from break-out groups, and prioritization
• 11.40am Future research avenues possibly enabled by this project: large-group brainstorming
• 12.30pm Adjourn

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

• We have started to 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.

Participants

Members of the project team are in bold font.

Name	Institution
Arhat Abzhanov	Department of Organismic and Evolutionary Biology, Harvard University
Jim Balhoff	NESCent
Wasila Dahdul	Department of Ichthyology, Academy of Natural Sciences
Hopi Hoekstra	Department of Organismic and Evolutionary Biology, Harvard University
Hans Hofmann	Dept. Integrative Biology, University of Texas at Austin
Elizabeth Jockusch	Department of Ecology & Evolutionary Biology, University of Connecticut
Elizabeth Kellogg	Dept. of Biology, University of Missouri - St. Louis
Chuck Kimmel	Institute of Neuroscience, University of Oregon
Hilmar Lapp	NESCent
John Lundberg	Department of Ichthyology, Academy of Natural Sciences
Paula Mabee	University of South Dakota
Austin Mast	Department of Biological Science, Florida State University
Peter Midford	Dept. of Ecology and Evolutionary Biology, University of Kansas
David Stern	Department of Ecology and Evolutionary Biology, Princeton University
Todd Vision	NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Gunter Wagner	Yale University
Monte Westerfield	Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon