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==
  
'''Venue: Sylvan Lake Lodge http://www.custerresorts.com/sylvan-lake-lodge-custer-state-park-resort/ South Dakota
+
'''Venue: South Dakota
 +
'''<span class="plainlinks">[http://www.radisson.com/rapidcitysd/ Radisson Hotel, Rapid City]</span> (Sept. 27-29)
 +
'''<span class="plainlinks">[http://www.custerresorts.com/sylvan-lake-lodge-custer-state-park-resort/ Sylvan Lake Lodge]</span>, South Dakota (Sept. 29-Oct.1)
  
 
'''Date:''' September 27-October 1, 2008
 
'''Date:''' September 27-October 1, 2008
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==Introduction==
 
==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.
+
Purpose:
  
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.
+
# 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
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.
+
# Project personnel meeting
  
 
==Agenda==
 
==Agenda==
  
Draft at ''[[Data_Jamboree_2/agenda]]'' for the program for each day.
+
See [[Data_Jamboree_2/Agenda|detailed agenda]] for the program for each day.
  
 
==Resources==
 
==Resources==
  
For curators:
+
For Participants
 +
* [[Phenex|Download Phenex]]
 
* [[Guide to Character Annotation]]
 
* [[Guide to Character Annotation]]
* [https://webdav.nescent.org/phenoscape-data/TaxonList_rev.doc Entering a taxon list]
+
* Curation Exercise instructions (forthcoming)
* [https://webdav.nescent.org/phenoscape-data/group-exercise.doc Group exercise instructions]
+
* [[Term_Requests | Term request instructions]]
* [[Phenote User Guide]] (this also contains detailed instructions for downloading and running Phenote)
+
**[http://sourceforge.net/tracker/?group_id=76834&atid=994764 link to submit Anatomy Requests]
* [[Resources for curators]]
+
**[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==
  
* For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millennium Hotel] (2800 Campus Walk Ave, Durham, NC  27705; tel. (919) 383-8575)
+
* <span class="plainlinks">[http://www.radisson.com/rapidcitysd/ Radisson Hotel, Rapid City]</span> (Sept. 27-29)
* For dining & entertainment, NESCent is right across from [http://www.ninthst.com/ Ninth Street]
+
* <span class="plainlinks">[http://www.custerresorts.com/sylvan-lake-lodge-custer-state-park-resort/ Sylvan Lake Lodge]</span> (Sept. 29-Oct.1)
* For the venue, NESCent is in the historic [http://www.owdna.org/mill.htm Erwin Mills] building (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>)
+
* [http://www.travelsd.com/about/events/buffaloroundup.asp Buffalo Roundup] (Sep 29)
 
+
* Travel agent: [mailto:Marybeth.Vlasman%40aaasd%2eorg Marybeth Vlasman] or [mailto:kristen.walker%40aaasd%2eorg Kristen Walker] at AAA travel
==Reading==
 
 
 
* We use the tag "<span class="plainlinks">[http://www.connotea.org/tag/phenoscape phenoscape]</span>" 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. [http://dx.doi.org/10.1016/j.tree.2007.03.013 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. [http://dx.doi.org/10.1002/jez.b.21181 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) [[Media:Caroreprint.pdf|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==
 
==Participants==
Line 53: Line 53:
 
! Name !! Institution
 
! Name !! Institution
 
{{EventParticipant|Balhoff|Jim|balhoff%40nescent%2eorg|NESCent|'''}}
 
{{EventParticipant|Balhoff|Jim|balhoff%40nescent%2eorg|NESCent|'''}}
{{EventParticipant|Coburn|Miles|coburn%40jcu%2eedu|John Carroll University|}}
+
{{EventParticipant|Blake|Judith|jblake%40informatics%2ejax.org|The Jackson Laboratory|}}
{{EventParticipant|Dahdul|Wasila|dahdul%40acnatsci%2eorg|Department of Ichthyology, Academy of Natural Sciences|'''}}
+
{{EventParticipant|Grande|Terry|TGRANDE%40luc%2eedu|Loyola University, Chicago|}}
 +
{{EventParticipant|Dahdul|Wasila|Wasila.Dahdul%40usd%2eedu|University of South Dakota and NESCent|'''}}
 +
{{EventParticipant|Engeman|Jeff|jeffrey%2eengeman%40usd%2eedu|University of South Dakota|}}
 +
{{EventParticipant|Hilton|Eric|ehilton%40vims%2eedu|Virginia Institute of Marine Science|}}
 +
{{EventParticipant|Kothari|Cartik|cartik%40nescent%2eorg|NESCent|'''}}
 
{{EventParticipant|Lapp|Hilmar|hlapp%40nescent%2eorg|NESCent|'''}}
 
{{EventParticipant|Lapp|Hilmar|hlapp%40nescent%2eorg|NESCent|'''}}
 +
{{EventParticipant|Lewis|Suzanna|lsuzi%40fruitfly2eorg |Berkeley Bioinformatics and Ontology Project|}}
 
{{EventParticipant|Lundberg|John|lundberg%40acnatsci%2eorg |Department of Ichthyology, Academy of Natural Sciences|'''}}
 
{{EventParticipant|Lundberg|John|lundberg%40acnatsci%2eorg |Department of Ichthyology, Academy of Natural Sciences|'''}}
 
{{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|University of South Dakota|'''}}
 
{{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|University of South Dakota|'''}}
 +
{{EventParticipant|Mayden|Rick|cypriniformes@gmail.com|St. Louis University|}}
 
{{EventParticipant|Midford|Peter|petermidford%40yahoo%2ecom|Dept. of Ecology and Evolutionary Biology, University of Kansas|'''}}
 
{{EventParticipant|Midford|Peter|petermidford%40yahoo%2ecom|Dept. of Ecology and Evolutionary Biology, University of Kansas|'''}}
 +
{{EventParticipant|Sabaj Pérez|Mark|sabaj%40acnatsci%2eorg|Academy of Natural Sciences, Philadelphia|}}
 
{{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|}}
 
|}
 
|}
  
 
==Papers for Annotation==
 
==Papers for Annotation==
*Miles Coburn
+
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 "<span class="plainlinks">[http://www.connotea.org/tag/phenoscape phenoscape]</span>" 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. [http://dx.doi.org/10.1016/j.tree.2007.03.013 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. [http://dx.doi.org/10.1002/jez.b.21181 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) [[Media:Caroreprint.pdf|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.
 +
 
 +
[[Category:Data Jamboree 2]]
 +
[[Category:Events]]

Latest revision as of 20:08, 1 March 2011

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

Notes

Consistency Experiment Results

Logistics

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.