• Data Jamboree 2
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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 DakotaRadisson 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 | |——|——————————|

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.