Needs Analysis Workshop

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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

Tuesday, September 18

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