Data Jamboree 2

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

A workshop hosted by the University of South Dakota and the National Evolutionary Synthesis Center (NESCent) through NSF-DBI "Phenoscape" grant funding.

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

See detailed agenda for the program for each day.

Resources

For Participants

• Download Phenex
• Guide to Character Annotation
• Curation Exercise instructions (forthcoming)
• Term request instructions
  • link to submit Anatomy Requests
  • link to submit Taxonomy Requests
• Additional resources for curator

Notes

Consistency Experiment Results

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
Mike Wallinga	University of South Dakota

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., and T. Grande. 2003. Ontogeny of the accessory neural arch in pristigasteroid clupeomorphs and its bearing on the homology of the otophysan claustrum (Teleostei). Copeia 2003:838-845.
  • Grande, T., and F. J. Poyato-Ariza. 1999. Phylogenetic relationships of fossil and Recent gonorynchiform fishes (Teleostei: Ostariophysi). Zoological Journal of the Linnean Society 125:197-238.
  • Poyato-Ariza, F. J. 1996. A revision of the ostariophysan fish family Chanidae, with special reference to the Mesozoic forms. Palaeo Ichthyologica 6:1-52.
  • Grande, T., and L. Grande. 2008. Reevaluation of the gonorynchiform genera Ramallichthys, Judeichthys and Notogoneus, with comments on the families Charitosomidae and Gonorynchidae. Mesozoic Fishes 4:295-310.

• Richard Mayden (Cypriniformes)
  • Mayden, R. L. 1989. Phylogenetic studies of North American minnows, with emphasis on the genus Cyprinella (Teleostei: Cypriniformes). University of Kansas Museum of Natural History Miscellaneous Publications 80:1-189.
  • Cavender, T. M., and M. M. Coburn. 1992. Phylogenetic relationships of North American Cyprinidae. Pp. 293-327 in R. L. Mayden, ed. Systematics, Historical Ecology, and North American Freshwater Fishes. Stanford University Press, Stanford.
  • Conway, K. W., and R. L. Mayden. 2007. The gill arches of Psilorhynchus (Ostariophysi: Psilorhynchidae). Copeia 2007: 267–280

• Eric Hilton (Clupeiformes and Ostariophysi)
  • Chang, Miman; Maisey, J. G. 2003. Redescription of †Ellimma branneri and †Diplomystus shengliensis, and Relationships of Some Basal Clupeomorphs. American Museum Novitates 3404:1-35.
  • Arratia, G. 1999. The monophyly of Teleostei and stem-group teleosts. Consensus and disagreements. Pp. 265-334 in G. Arratia, and H.-P. Schultze, eds. Mesozoic Fishes 2- Systematics and Fossil Record. Verlag Dr. F. Pfeil, Munchen.

• Mark Sabaj Pérez (Siluriformes)
  • De Pinna, M. C. C. 1993. Higher-level Phylogeny of Siluriformes (Teleostei: Ostariophysi), with a New Classification of the Order. City University of New York, New York.
  • Mo, T. 1991. Anatomy, Relationships and Systematics of the Bagridae (Teleostei: Siluroidei) with a Hypothesis of Siluroid Phylogeny, Theses Zoologicae, 17, Koeltz, Koenigstein.
  • De Pinna, M. C. C. 1996. A phylogenetic analysis of the Asian catfish families Sisoridae, Akysidae, and Amblycipitidae, with a hypothesis on the relationships of the neotropical Aspredinidae (Teleostei, Ostariophysi). Fieldiana: Zoology (New Series) 84:i–iv + 1-83.

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.