Difference between revisions of "Skeletal Anatomy Jamboree"

From phenoscape
(→‎Reading)
(→‎Download the Vertebrate Anatomy Ontology)
 
(42 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
<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
−
* 8:45-9:30 Welcomes and participant introductions (2-3 minute lightening talks)
+
* 9:00-9:30 Welcomes and participant introductions (2-3 minute lightning talks)
−
* 9:30-10:00 Paula Mabee: Introduction to workshop
+
* 9:30-9:45 [[Media:Mabee-Skeletal.pdf|Paula Mabee]]: Introduction to workshop
−
* 10:00-10:15 Wasila Dahdul: Introduction to ontologies and skeletal anatomy issues
+
* 9:45-10:00 [[Media:Hall-Skeletal.pdf|Brian Hall]]: Introduction to bone classification
−
* 10:15-10:30 Alex Diehl: Introduction to Cell Ontology and cross-products
+
* 10:00-10:15 [[Media:Haendel-CARO-skeletal.pdf|Melissa Haendel]]: Common Anatomy Reference Ontology and bone classification
−
* 10:30  Coffee break
+
* 10:15 Coffee break
−
* 10:30-10:45 Brian Hall: Intro to bone classification
+
* 10:45-11:00 [[Media:Diehl-CL-skeletal.pdf|Alex Diehl]]: Introduction to Cell Ontology and cross-products
−
* 10:45-11:45  Group discussion on use cases
+
* 11:00-11:15 [[Media:Dahdul-skelelal.pdf|Wasila Dahdul]]: Introduction to ontologies and skeletal anatomy issues
−
* 11:45-12:15
+
* 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''' -- breakout groups TBD
+
'''Afternoon'''
−
* 1:30 – 2:00
+
''User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)''
−
* 2:00 - 3:15
+
* 1:30 – 3:00 Break out groups
−
* 3:15 Coffee break
+
* 3:00 Coffee break
−
* 3:30-4:15:
+
* 3:15-4:30 Reports from break out groups and ontology editing
−
* 4:15-5:00:
+
* 4:30 NESCent reception
−
* 5:00: Van back to hotel
+
* 5:30 Shuttle back to hotel
−
* 5:30-6:30: Drinks at hotel
+
* 6:30 Shuttle from hotel to [http://2ndfridayartwalk.com/ Carrboro Art Walk]
−
* 6:30 Van from hotel to dinner (whole group)
+
* 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'''
−
* 8:00 SHUTTLE FROM HOTEL
+
* 8:30 SHUTTLE FROM HOTEL
−
* 8:15 Coffee & pastries
+
* 8:45 Coffee & pastries
−
* 8:30-9:30
+
* 9:00-10:30 continue break out groups
−
* 9:30-9:45
+
* 10:30 Coffee
−
* 9:45
+
* 11:00-12:15 Reports from break out groups; ontology editing
−
* 10:45 Coffee
 
−
* 11:00-11:45    Phenoscape Knowledgebase usability testing concurrent with breakout groups
 
−
* 11:45-12:15
 
 
* 12:15 LUNCH
 
* 12:15 LUNCH
  
 
'''Afternoon'''
 
'''Afternoon'''
−
* 1:30 – 2:00:
+
''User interface testing concurrent with breakout groups (Peter Midford and Jim Balhoff)''
−
* 2:00
+
* 1:30-3:15 continue break out groups
 
* 3:15 Coffee break
 
* 3:15 Coffee break
−
* 3:30-4:15:
+
* 3:45-5:00 Reports from break out groups; ontology editing
−
* 4:15-5:00:
+
* 5:00-5:30 Wrap up
−
* 5:00: Van back to hotel
+
* 5:30 Van back to hotel
−
* 5:30-6:30: Drinks at hotel
+
* 6:15 Van from hotel to dinner [http://www.pops-durham.com/ Pop's]
−
* 6:30 Van from hotel to dinner (whole group)
 
  
 
=== 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://www.ninthst.com/ Ninth Street]
+
* 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., 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://dx.doi.org/10.1093/sysbio/syq013 doi:10.1093/sysbio/syq013]
+
# 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 P, Ashburner M, Cronk Q, Gkoutos G, Haendel M, et al. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution 22: 345-350.
+
# 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, 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.
 
# 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 ==
 
== Participants ==
Line 88: Line 94:
 
! Name !! Institution
 
! Name !! Institution
 
{{EventParticipant|Balhoff|Jim|balhoff@nescent.org|Phenoscape and NESCent|'''}}
 
{{EventParticipant|Balhoff|Jim|balhoff@nescent.org|Phenoscape and NESCent|'''}}
−
{{EventParticipant|Blackburn|David|david.c.blackburn@gmail.com|Amphibian Anatomy Ontology and University of Kansas|}}
+
{{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|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|Diehl|Alexander|adiehl@informatics.jax.org|Mouse Genome Informatics (MGI)|}}
Line 97: Line 103:
 
{{EventParticipant|Midford|Peter|peter%2emidford%40gmail%2ecom| Phenoscape and NESCent|'''}}
 
{{EventParticipant|Midford|Peter|peter%2emidford%40gmail%2ecom| Phenoscape and NESCent|'''}}
 
{{EventParticipant|Ringwald|Martin|ringwald@informatics.jax.org|Mouse Genome Informatics (MGI)|}}
 
{{EventParticipant|Ringwald|Martin|ringwald@informatics.jax.org|Mouse Genome Informatics (MGI)|}}
−
{{EventParticipant|Segerdell|Erik|segerdel@ohsu.edu|Oregon Health Sciences University|}}
+
{{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|Van Slyke|Ceri|van_slyke@zfin.org|Zebrafish Information Network (ZFIN)|}}
 
{{EventParticipant|Vickaryous|Matt|mvickary@uoguelph.ca|Ontario Veterinary College, University of Guelph|}}
 
{{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 |'''}}
 
{{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

Phenoscape Skeletal Anatomy Jamboree: April 9-10, 2010

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

  1. 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)
  2. 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
  3. 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
  4. 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.
  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
Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Skeletal_Anatomy_Jamboree&oldid=10151"