Difference between revisions of "Skeletal Anatomy Jamboree"
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| − | <center><big>'''Phenoscape Skeletal Anatomy Jamboree: April 9-10, 2010'''</big><br/><br/>A workshop hosted by the National Evolutionary Synthesis Center (NESCent)</center> | + | <center><big>'''Phenoscape Skeletal Anatomy Jamboree: April 9-10, 2010'''</big><br/><br/>A Phenoscape workshop (NSF grant BDI-0641025) hosted by the National Evolutionary Synthesis Center (NESCent)</center> |
__NOTOC__ | __NOTOC__ | ||
| Line 5: | Line 5: | ||
== Location and Date == | == Location and Date == | ||
| − | '''Venue:''' National Evolutionary Synthesis Center (NESCent) (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>, also see <span class="plainlinks">[http://www.nescent.org/about/information.php information for visitors]</span>) | + | '''Venue:''' National Evolutionary Synthesis Center (NESCent), Durham, NC (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>, also see <span class="plainlinks">[http://www.nescent.org/about/information.php information for visitors]</span>) |
'''Date:''' April 9-10, 2010 | '''Date:''' April 9-10, 2010 | ||
| Line 13: | Line 13: | ||
== Introduction == | == Introduction == | ||
The main focus of this meeting will be to re-evaluate the high-level skeletal system ontology hierarchy for fishes, particularly in relation to anatomy ontologies of other vertebrates. We will re-examine existing terms and definitions (cells, tissues, development, anatomical structures) for their applicability across vertebrates and redefine terms as necessary so that we leave with complete definitions. We will discuss how to represent of bone development within the structurally-defined hierarchy of the anatomy ontology. In addition, ontological issues such as multiple inheritance and cross-product definitions will be discussed although their solutions depend on the definitions we develop for the relevant terms. | The main focus of this meeting will be to re-evaluate the high-level skeletal system ontology hierarchy for fishes, particularly in relation to anatomy ontologies of other vertebrates. We will re-examine existing terms and definitions (cells, tissues, development, anatomical structures) for their applicability across vertebrates and redefine terms as necessary so that we leave with complete definitions. We will discuss how to represent of bone development within the structurally-defined hierarchy of the anatomy ontology. In addition, ontological issues such as multiple inheritance and cross-product definitions will be discussed although their solutions depend on the definitions we develop for the relevant terms. | ||
| + | |||
| + | == Download the Vertebrate Anatomy Ontology == | ||
| + | Download current release version in [http://purl.obolibrary.org/obo/vsao.obo OBO] or [http://purl.obolibrary.org/obo/vsao.owl OWL] format. | ||
| + | |||
| + | Download the version generated from discussion at the workshop [https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/vocab/VSAO-workshop.obo here] | ||
== Agenda == | == Agenda == | ||
| Line 20: | Line 25: | ||
* 8:30 SHUTTLE FROM HOTEL | * 8:30 SHUTTLE FROM HOTEL | ||
* 8:45 Coffee & pastries | * 8:45 Coffee & pastries | ||
| − | * | + | * 9:00-9:30 Welcomes and participant introductions (2-3 minute lightning talks) |
| − | * 9: | + | * 9:30-9:45 [[Media:Mabee-Skeletal.pdf|Paula Mabee]]: Introduction to workshop |
| − | * 9:45-10: | + | * 9:45-10:00 [[Media:Hall-Skeletal.pdf|Brian Hall]]: Introduction to bone classification |
| − | * 10: | + | * 10:00-10:15 [[Media:Haendel-CARO-skeletal.pdf|Melissa Haendel]]: Common Anatomy Reference Ontology and bone classification |
| − | * 10: | + | * 10:15 Coffee break |
| − | * 10:45-11:45 Group discussion on use cases | + | * 10:45-11:00 [[Media:Diehl-CL-skeletal.pdf|Alex Diehl]]: Introduction to Cell Ontology and cross-products |
| − | * 11:45-12:15 | + | * 11:00-11:15 [[Media:Dahdul-skelelal.pdf|Wasila Dahdul]]: Introduction to ontologies and skeletal anatomy issues |
| + | * 11:15-11:45 Group discussion on use cases | ||
| + | * 11:45-12:00 Wrap up and devise breakout groups for afternoon | ||
| + | * 12:00-12:15 Jim Balhoff: Introduction to Phenoscape Knowledgebase interfaces and mockups | ||
* 12:15 LUNCH | * 12:15 LUNCH | ||
| − | '''Afternoon''' | + | '''Afternoon''' |
| − | * 1:30 – | + | ''User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)'' |
| − | * | + | * 1:30 – 3:00 Break out groups |
| − | + | * 3:00 Coffee break | |
| − | * 3: | + | * 3:15-4:30 Reports from break out groups and ontology editing |
| − | * 4: | + | * 4:30 NESCent reception |
| − | * 5: | + | * 5:30 Shuttle back to hotel |
| − | * | + | * 6:30 Shuttle from hotel to [http://2ndfridayartwalk.com/ Carrboro Art Walk] |
| − | * | + | * 8:30 Dinner at [http://www.crookscorner.com/ Crook's Corner] |
| + | * 10:00 Shuttle back to hotel | ||
=== Saturday, April 10, 2010 === | === Saturday, April 10, 2010 === | ||
'''Morning''' | '''Morning''' | ||
| − | * 8: | + | * 8:30 SHUTTLE FROM HOTEL |
| − | * 8: | + | * 8:45 Coffee & pastries |
| − | * | + | * 9:00-10:30 continue break out groups |
| − | * | + | * 10:30 Coffee |
| − | + | * 11:00-12:15 Reports from break out groups; ontology editing | |
| − | |||
| − | * 11:00 | ||
| − | |||
* 12:15 LUNCH | * 12:15 LUNCH | ||
'''Afternoon''' | '''Afternoon''' | ||
| − | * 1:30 | + | ''User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)'' |
| − | + | * 1:30-3:15 continue break out groups | |
* 3:15 Coffee break | * 3:15 Coffee break | ||
| − | * 3: | + | * 3:45-5:00 Reports from break out groups; ontology editing |
| − | * | + | * 5:00-5:30 Wrap up |
| − | * 5: | + | * 5:30 Van back to hotel |
| − | * | + | * 6:15 Van from hotel to dinner [http://www.pops-durham.com/ Pop's] |
| − | |||
=== Sunday, April 11, 2010 === | === Sunday, April 11, 2010 === | ||
* Participants leave | * Participants leave | ||
| + | |||
| + | * 9-12 Phenoscape project meeting | ||
== Logistics == | == Logistics == | ||
* For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millennium Hotel] (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575) | * For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millennium Hotel] (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575) | ||
| − | * For dining & entertainment, NESCent is right across from [http:// | + | * For dining & entertainment, NESCent is right across from [http://maps.google.com/maps?f=l&hl=en&q=restaurants&near=9th+st+and+w+main+durham&ie=UTF8&om=1&ll=36.008093,-78.921983&spn=0.00723,0.012145&z=17 Ninth Street] |
* 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>) | * 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>) | ||
== Reading == | == Reading == | ||
| − | # Hall, B. K., and Witten, P. E. (2007). The Origin and Plasticity of Skeletal Tissues in Vertebrate Evolution and Development. In: Major Transitions in Vertebrate Evolution (Jason S. Anderson and Hans-Dieter Sues, eds). Festschrift for Dr. Robert L. Carroll. pp. 13-57. Indiana University Press, Bloomington, IN. | + | # Hall, B. K., and Witten, P. E. (2007). The Origin and Plasticity of Skeletal Tissues in Vertebrate Evolution and Development. In: Major Transitions in Vertebrate Evolution (Jason S. Anderson and Hans-Dieter Sues, eds). Festschrift for Dr. Robert L. Carroll. pp. 13-57. Indiana University Press, Bloomington, IN.(You should have gotten a copy of this by email; let us know if you need it) |
| − | # Dahdul, W. M., J. G. | + | # Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. (2010) The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology. [http://sysbio.oxfordjournals.org/cgi/content/abstract/syq013?ijkey=MlgvHlLnxCRnvPo&keytype=ref doi:10.1093/sysbio/syq013] |
| − | # Mabee | + | # 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] |
| − | # Haendel | + | # 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. |
| − | # Hall, B. 2005. Bones and Cartilage: Developmental Skeletal Biology. Academic Press. 792 p. | + | # Hall, B. 2005. Bones and Cartilage: Developmental Skeletal Biology. Academic Press. 792 p. ISBN 978-0-12-319060-4. |
| + | |||
| + | == Participants == | ||
| + | |||
| + | Members of Phenoscape are in '''bold font'''. | ||
| + | |||
| + | {| border="1" cellpadding="3" cellspacing="0" | ||
| + | |- | ||
| + | ! Name !! Institution | ||
| + | {{EventParticipant|Balhoff|Jim|balhoff@nescent.org|Phenoscape and NESCent|'''}} | ||
| + | {{EventParticipant|Blackburn|David|david.c.blackburn@gmail.com|Amphibian Anatomy Ontology (AmphibAnat) and University of Kansas|}} | ||
| + | {{EventParticipant|Dahdul|Wasila|wasila.dahdul@usd.edu|Phenoscape, NESCent and University of South Dakota|'''}} | ||
| + | {{EventParticipant|Diehl|Alexander|adiehl@informatics.jax.org|Mouse Genome Informatics (MGI)|}} | ||
| + | {{EventParticipant|Haendel|Melissa|haendel@ohsu.edu|Oregon Health Sciences University|}} | ||
| + | {{EventParticipant|Hall|Brian|Brian.Hall@Dal.Ca|Department of Biology, Dalhousie University|}} | ||
| + | {{EventParticipant|Lundberg|John|lundberg@ansp.org|Phenoscape and Department of Ichthyology, Academy of Natural Sciences, Philadelphia|'''}} | ||
| + | {{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|Phenoscape and Department of Biology, University of South Dakota|'''}} | ||
| + | {{EventParticipant|Midford|Peter|peter%2emidford%40gmail%2ecom| Phenoscape and NESCent|'''}} | ||
| + | {{EventParticipant|Ringwald|Martin|ringwald@informatics.jax.org|Mouse Genome Informatics (MGI)|}} | ||
| + | {{EventParticipant|Segerdell|Erik|segerdel@ohsu.edu|Oregon Health Sciences University (representing Xenbase)|}} | ||
| + | {{EventParticipant|Van Slyke|Ceri|van_slyke@zfin.org|Zebrafish Information Network (ZFIN)|}} | ||
| + | {{EventParticipant|Vickaryous|Matt|mvickary@uoguelph.ca|Ontario Veterinary College, University of Guelph|}} | ||
| + | {{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu| Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon |'''}} | ||
| + | |} | ||
| + | |||
| + | [[Category:Events]] | ||
| + | [[Category:Anatomy]] | ||
| + | [[Category:Ontology]] | ||
Latest revision as of 20:15, 17 August 2012
A Phenoscape workshop (NSF grant BDI-0641025) hosted by the National Evolutionary Synthesis Center (NESCent)
Location and Date
Venue: National Evolutionary Synthesis Center (NESCent), Durham, NC (directions, also see information for visitors)
Date: April 9-10, 2010
Organizers: Paula Mabee, Wasila Dahdul
Introduction
The main focus of this meeting will be to re-evaluate the high-level skeletal system ontology hierarchy for fishes, particularly in relation to anatomy ontologies of other vertebrates. We will re-examine existing terms and definitions (cells, tissues, development, anatomical structures) for their applicability across vertebrates and redefine terms as necessary so that we leave with complete definitions. We will discuss how to represent of bone development within the structurally-defined hierarchy of the anatomy ontology. In addition, ontological issues such as multiple inheritance and cross-product definitions will be discussed although their solutions depend on the definitions we develop for the relevant terms.
Download the Vertebrate Anatomy Ontology
Download current release version in OBO or OWL format.
Download the version generated from discussion at the workshop here
Agenda
Friday, April 9, 2010
Morning
- 8:30 SHUTTLE FROM HOTEL
- 8:45 Coffee & pastries
- 9:00-9:30 Welcomes and participant introductions (2-3 minute lightning talks)
- 9:30-9:45 Paula Mabee: Introduction to workshop
- 9:45-10:00 Brian Hall: Introduction to bone classification
- 10:00-10:15 Melissa Haendel: Common Anatomy Reference Ontology and bone classification
- 10:15 Coffee break
- 10:45-11:00 Alex Diehl: Introduction to Cell Ontology and cross-products
- 11:00-11:15 Wasila Dahdul: Introduction to ontologies and skeletal anatomy issues
- 11:15-11:45 Group discussion on use cases
- 11:45-12:00 Wrap up and devise breakout groups for afternoon
- 12:00-12:15 Jim Balhoff: Introduction to Phenoscape Knowledgebase interfaces and mockups
- 12:15 LUNCH
Afternoon User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)
- 1:30 – 3:00 Break out groups
- 3:00 Coffee break
- 3:15-4:30 Reports from break out groups and ontology editing
- 4:30 NESCent reception
- 5:30 Shuttle back to hotel
- 6:30 Shuttle from hotel to Carrboro Art Walk
- 8:30 Dinner at Crook's Corner
- 10:00 Shuttle back to hotel
Saturday, April 10, 2010
Morning
- 8:30 SHUTTLE FROM HOTEL
- 8:45 Coffee & pastries
- 9:00-10:30 continue break out groups
- 10:30 Coffee
- 11:00-12:15 Reports from break out groups; ontology editing
- 12:15 LUNCH
Afternoon User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)
- 1:30-3:15 continue break out groups
- 3:15 Coffee break
- 3:45-5:00 Reports from break out groups; ontology editing
- 5:00-5:30 Wrap up
- 5:30 Van back to hotel
- 6:15 Van from hotel to dinner Pop's
Sunday, April 11, 2010
- Participants leave
- 9-12 Phenoscape project meeting
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
- Hall, B. K., and Witten, P. E. (2007). The Origin and Plasticity of Skeletal Tissues in Vertebrate Evolution and Development. In: Major Transitions in Vertebrate Evolution (Jason S. Anderson and Hans-Dieter Sues, eds). Festschrift for Dr. Robert L. Carroll. pp. 13-57. Indiana University Press, Bloomington, IN.(You should have gotten a copy of this by email; let us know if you need it)
- Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., Mabee, P.M. (2010) The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology. doi:10.1093/sysbio/syq013
- 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
- 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.
- Hall, B. 2005. Bones and Cartilage: Developmental Skeletal Biology. Academic Press. 792 p. ISBN 978-0-12-319060-4.
Participants
Members of Phenoscape are in bold font.
| Name | Institution |
|---|---|
| Jim Balhoff | Phenoscape and NESCent |
| David Blackburn | Amphibian Anatomy Ontology (AmphibAnat) and University of Kansas |
| Wasila Dahdul | Phenoscape, NESCent and University of South Dakota |
| Alexander Diehl | Mouse Genome Informatics (MGI) |
| Melissa Haendel | Oregon Health Sciences University |
| Brian Hall | Department of Biology, Dalhousie University |
| John Lundberg | Phenoscape and Department of Ichthyology, Academy of Natural Sciences, Philadelphia |
| Paula Mabee | Phenoscape and Department of Biology, University of South Dakota |
| Peter Midford | Phenoscape and NESCent |
| Martin Ringwald | Mouse Genome Informatics (MGI) |
| Erik Segerdell | Oregon Health Sciences University (representing Xenbase) |
| Ceri Van Slyke | Zebrafish Information Network (ZFIN) |
| Matt Vickaryous | Ontario Veterinary College, University of Guelph |
| Monte Westerfield | Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon |
