Data Jamboree 1
**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:
Notes and annotation results:
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:
- 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>
- 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>
- 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 |
|——|—————————|
Papers for Annotation
- 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.
- 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.
- Hoffmann, M. and R. Britz. 2006. Ontogeny and homology of the neural
complex of otophysan Ostariophysi. Zool. J. Linn. Soc.
147(3):301-330.
- 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.
- Sawada, Y. 1982. Phylogeny and zoogeography of the superfamily
Cobitoidea (Cyprinoidei: Cypriniformes). Mem. Fact. Fish. Hokkaido
Univ. 28:65-223.
- 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
- Conway, K. W., and R. L. Mayden. 2007. Gill Arches of Psilorhynchus
(Ostariophysi: Psilorhynchidae). Copeia: 2007:267-280
- Conway, K. W. 2005. Monophyly of the genus Boraras (Teleostei:
Cyprinidae). Ichthyological Exploration of Freshwaters 16(3):
249-264.
- 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.
- 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.
- 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.
- 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.
- de Pinna MCC. 1996. Teleostean monophyly Interrelationships of
Fishes. New York: Academic Press. 147-162.
- Sidlauskas B, Vari RP. in press. Phylogenetic relationships within
the South American fish family Anostomidae (Teleostei, Ostariophysi,
Characiformes). Zoological Journal of the Linnean Society.
- 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.