Difference between revisions of "Data Jamboree 2"
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− | <center><big>'''Linking Evolution to Genomics Using Phenotype Ontologies:'''<br/>'''Second Morphology Data Jamboree'''</big><br/><br/>A workshop hosted by the National Evolutionary Synthesis Center (NESCent).</center> | + | <center><big>'''Linking Evolution to Genomics Using Phenotype Ontologies:'''<br/>'''Second Morphology Data Jamboree'''</big><br/><br/>A workshop hosted by the University of South Dakota and the National Evolutionary Synthesis Center (NESCent) through NSF-DBI "Phenoscape" grant funding.</center> |
==Location and Date== | ==Location and Date== | ||
Line 21: | Line 21: | ||
==Agenda== | ==Agenda== | ||
− | + | See [[Data_Jamboree_2/Agenda|detailed agenda]] for the program for each day. | |
==Resources== | ==Resources== | ||
− | For | + | For Participants |
+ | * [[Phenex|Download Phenex]] | ||
* [[Guide to Character Annotation]] | * [[Guide to Character Annotation]] | ||
− | * [ | + | * Curation Exercise instructions (forthcoming) |
− | * [https:// | + | * [[Term_Requests | Term request instructions]] |
− | + | **[http://sourceforge.net/tracker/?group_id=76834&atid=994764 link to submit Anatomy Requests] | |
− | + | **[http://sourceforge.net/tracker/?atid=1046550&group_id=76834&func=browse link to submit Taxonomy Requests] | |
+ | * [[Resources for curators | Additional resources for curator]] | ||
+ | |||
+ | [https://www.nescent.org/phenoscape/Data_Jamboree_2/Notes Notes] | ||
+ | |||
+ | [[Data_Jamboree_2/Annotation_Experiment | Consistency Experiment Results]] | ||
==Logistics== | ==Logistics== | ||
Line 62: | Line 68: | ||
{{EventParticipant|Vision|Todd|tjv%40bio%2eunc%2eedu|NESCent, and Department of Biology, University of North Carolina at Chapel Hill|'''}} | {{EventParticipant|Vision|Todd|tjv%40bio%2eunc%2eedu|NESCent, and Department of Biology, University of North Carolina at Chapel Hill|'''}} | ||
{{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu|Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon|'''}} | {{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu|Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon|'''}} | ||
+ | {{EventParticipant|Wallinga|Mike|mwalling@nwciowa.edu|University of South Dakota|}} | ||
|} | |} | ||
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*Terry Grande (Gonorynchiformes and Ostariophysi) | *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. | + | **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. | + | **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) | *Richard Mayden (Cypriniformes) | ||
− | **Mayden ( | + | **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 | + | **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 | + | **Conway, K. W., and R. L. Mayden. 2007. The gill arches of ''Psilorhynchus'' (Ostariophysi: Psilorhynchidae). Copeia 2007: 267–280 |
*Eric Hilton (Clupeiformes and Ostariophysi) | *Eric Hilton (Clupeiformes and Ostariophysi) | ||
− | **Chang, | + | **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 | + | **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) | *Mark Sabaj Pérez (Siluriformes) | ||
Line 96: | Line 103: | ||
[[Category:Data Jamboree 2]] | [[Category:Data Jamboree 2]] | ||
+ | [[Category:Events]] |
Latest revision as of 20:08, 1 March 2011
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.
Contents
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:
- Evaluation of prototypes for web user interface
- Character data entry by experts; introduce new curators to Phenote and data entry; test/enhance curation consistency; further refine curation interface
- 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
- Additional resources for curator
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:
- 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.