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

Date: September 27-31, 2008

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

Introduction

We have developed the software tools to input systematic character data in a formalized way to a degree that we have started to enter species-level as well as some of the higher level taxonomic characters (e.g. from Fink & Fink, 1981). This workshop brings together morphologists from the community of ichthyologists and project personnel focused on morphology, taxonomy, data curation, ontology curation, and informatics. The workshop will introduce ichthyologists to the approach, and pair morphologists from the community with project personnel to work one-on-one on entering published systematic character data.

The hands-on curation work at the jamboree will almost certainly reveal ontological issues, such as terminology and synonymies, issues in annotation consistency or workflow, as well as usability and data flow issues involving the software tools. These will help drive the development of the database and web-based interfaces, but will also spur further development of the involved ontologies and refinement of the annotation procedures. The informatics as well as ontology personnel of the project will be on hand to respond to the issues on the spot.

Finally, the workshop will also provide a very interesting opportunity to brainstorm about the informatics tools and data required to push beyond current limits, thus fostering new discoveries at the interface between evolution and developmental genetics.

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

• 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 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
Jim Balhoff	NESCent
Miles Coburn	John Carroll University
Wasila Dahdul	Department of Ichthyology, Academy of Natural Sciences
Hilmar Lapp	NESCent
John Lundberg	Department of Ichthyology, Academy of Natural Sciences
Paula Mabee	University of South Dakota
Peter Midford	Dept. of Ecology and Evolutionary Biology, University of Kansas
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

• Miles Coburn