Data Jamboree 1

The final report from this event is available here.

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

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: April 18-20, 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

The Jamboree will start in the morning (~9am) on Friday, April 18, and continue through noon on Sunday, April 20. Non-project participants will arrive on Thursday, April 17, and depart in the afternoon of April 20. Please see the detailed 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

Notes and annotation results:

• Minutes from the jamboree (password protected)
• Minutes from the project meeting (password protected)
• Annotation Experiment results
• Final report

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
Kevin Conway	St. Louis 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
Mário de Pinna	Universidade de São Paulo
Martin Ringwald	The Jackson Laboratory
Brian Sidlauskas	NESCent
Todd Vision	NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Nicole Washington	Lawrence Berkeley National Lab
Monte Westerfield	Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon

Papers for Annotation

• Miles Coburn

1. Cavender, Ted M., and Miles M. Coburn. 1992. Phylogenetic relationships of North American Cyprinidae. Pp. 293-327. In: Systematics, Historical Ecology, and North American Freshwater Fishes. R.L. Mayden (Ed.). Stanford University Press. Stanford, California. 969 p.
2. Coburn, Miles M., and Ted M. Cavender. 1992. Interrelationships of North American cyprinid fishes. Pp. 328-373 In: Systematics, Historical Ecology, and North American Freshwater Fishes. R.L. Mayden (Ed.). Stanford University Press. Stanford, California. 969 p.
3. Hoffmann, M. and R. Britz. 2006. Ontogeny and homology of the neural complex of otophysan Ostariophysi. Zool. J. Linn. Soc. 147(3):301-330.
4. Weitzman, S.H. 1962. The osteology of Brycon meeki, a generalized characid fish, with an osteological definition of the family. Stanford Ichthy. Bull. 8(1): 1-77.
5. Sawada, Y. 1982. Phylogeny and zoogeography of the superfamily Cobitoidea (Cyprinoidei: Cypriniformes). Mem. Fact. Fish. Hokkaido Univ. 28:65-223.

• Kevin Conway

1. Conway, K. W., W-J Chen, and R. L. Mayden. 2008. The “Celestial Pearl danio” is a miniature Danio (s.s) (Ostariophysi: Cyprinidae): evidence from morphology and molecules. Zootaxa 1686:1-28
2. Conway, K. W., and R. L. Mayden. 2007. Gill Arches of Psilorhynchus (Ostariophysi: Psilorhynchidae). Copeia: 2007:267-280
3. Conway, K. W. 2005. Monophyly of the genus Boraras (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 16(3): 249-264.

• Mario de Pinna

1. de Pinna MCC. 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: 1-83.
2. de Pinna MCC, Ferraris CJJ, Vari RP. 2007. A phylogenetic study of the neotropical catfish family Cetopsidae (Osteichthys, Ostariophysi, Siluriformes), with a new classification. Zoological Journal of the Linnean Society 150: 755-813.
3. de Pinna MCC. 1992. A new subfamily of Trichomycteridae (Teleostei, Siluriformes), lower loricarioid relationships and a discussion on the impact of additional taxa for phylogenetic analysis. Zoological Journal of the Linnean Society 106: 175-229.
4. de Pinna MCC, Grande T. 2003. Ontogeny of the accessory neural arch in pristigasteroid clupeomorphs and its bearing on the homology of the otophysan claustrum (Teleostei). Copeia: 838-845.
5. de Pinna MCC. 1996. Teleostean monophyly Interrelationships of Fishes. New York: Academic Press. 147-162.

• B. Sidlauskas

1. Sidlauskas B, Vari RP. in press. Phylogenetic relationships within the South American fish family Anostomidae (Teleostei, Ostariophysi, Characiformes). Zoological Journal of the Linnean Society.
2. Vari RP, Castro RMC, Raredon SJ. 1995. The Neotropical fish family Chilodontidae (Teleostei: Characiformes): a phylogenetic study and a revision of Caenotropus Günther. Smithsonian Contributions to Zoology 577: 32.