Needs Analysis Workshop

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Revision as of 16:18, 19 September 2007 by Hilmar (talk | contribs) (Agenda)
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


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.


Monday, August 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
  • 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, August 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 (20mins per group)
  • 11.10am Future research avenues possibly enabled by this project: large-group brainstorming
  • 12pm Adjourn


  • 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)


  • We have started to use the tag "phenomap" 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.


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
Jim Hanken Museum of Comparative Zoology, Harvard University
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