Difference between revisions of "Phenotype Ontology Coordination Workshop"

From phenoscape
(Participants)
(Final report)
 
(23 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<center><big>'''Phenotype Ontology Coordination Workshop'''</big><br/><br/>A workshop hosted by the National Evolutionary Synthesis Center (NESCent)</center>
+
<center><big>'''Phenotype Ontology Coordination Workshop: April 27-28, 2009'''</big><br/><br/>A workshop hosted by the National Evolutionary Synthesis Center (NESCent)</center>
  
 
__NOTOC__
 
__NOTOC__
Line 7: Line 7:
 
'''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) (<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:''' Arpil 27-28, 2009
+
'''Date:''' April 27-28, 2009
  
 
'''Organizers:''' Paula Mabee, Monte Westerfield, Todd Vision
 
'''Organizers:''' Paula Mabee, Monte Westerfield, Todd Vision
Line 18: Line 18:
  
 
== Agenda ==
 
== Agenda ==
 
''Note that this agenda is still in draft stage and may change before the meeting.''
 
 
 
=== Monday, Apr. 27, 2009 ===
 
=== Monday, Apr. 27, 2009 ===
  
Line 29: Line 26:
 
* 8:00 SHUTTLE FROM HOTEL
 
* 8:00 SHUTTLE FROM HOTEL
 
* 8:15 Coffee & pastries
 
* 8:15 Coffee & pastries
* 8:30 Welcomes from NESCent (Todd Vision) and participant introductions (2-3 minute lightening talks)
+
* 8:30-9:30 Welcomes from NESCent (Todd Vision) and participant introductions (2-3 minute lightening talks)
* 9:00 Paula Mabee: Introduction: current phenotype ontology communities (MOD, Evo), where we stand in terms of ontologies and related databases, possibilities for where we go in the next 3-5 years, description of Interop vs. RCN, workshop goals
+
* 9:30-9:45 Paula Mabee: Introduction
* 9:30-10:15 Breakout groups and topics (need note-taker in each group):
+
* 9:45 Breakout groups (4 groups, all 4 questions each):
*# Taxonomy group: Do we need taxonomy ontologies for individual groups or a single reference ontology?  How to ensure interoperability with NCBI taxonomy ontology and associated molecular data (given EvoD need to represent extinct species) – with EoL/GBIF/etc and associated geospatial data? What specific steps should be taken to support the development of taxonomy ontologies and these integrative activities within the context of a phenotype consortium grant?
+
* Breakout questions: Tools (software), standards, and ontologies
*# Morphology group: How do existing common ontologies (AOs, PATO, CARO, Spatial, institutional collections codes, evidence code) need to be extended? How should multispecies anatomy ontologies be developed in relation to MOD anatomy ontologies, and how should synchrony be maintained?
+
* 1. What are the key gaps in tools to develop your work?
*# Ontologies with common time representation problem (developmental time, evolutionary time, paleontology, behavior): Is this a separate ‘core’?  Is it useful to generalize this problem and find common solutions?  Will it enhance interoperability?
+
* 2. What are key obstacles to data exchange and data integration?
* 10:15-10:45 Group reports
+
* 3. What do you perceive as the key ontologies that are lacking?
* 10:45 COFFEE
+
* 4. What are the gaps in expertise in understanding, developing and applying ontologies in the community?
* 11:00-11:45 Taxonomy, Morphology, and Ontologies/time break out groups (different participants in each)
+
* 10:45 Coffee
 +
* 11:00-11:45 Second breakout (2 groups, 2 questions each)
 
* 11:45-12:15 Reports from break-out groups
 
* 11:45-12:15 Reports from break-out groups
 
* 12:15 LUNCH
 
* 12:15 LUNCH
Line 47: Line 45:
 
*# Annotation group: What phenotype curation/annotation needs are there that are not adequately met?  E.g. software, standards, best-practices, education, syntax, etc.
 
*# Annotation group: What phenotype curation/annotation needs are there that are not adequately met?  E.g. software, standards, best-practices, education, syntax, etc.
 
*# Interoperability group 1 (MOD-EvoD): Develop a plan for interoperability between MODs and EvoDs through ontology synchronization and alignment
 
*# Interoperability group 1 (MOD-EvoD): Develop a plan for interoperability between MODs and EvoDs through ontology synchronization and alignment
*# Interoperability group 2 (MOD-EvoD): Develop a plan for interoperability among EvoDs, and with other community resources through alignment, considering the types of driving research questions (similarity searches on function, homology, etc.).  What are the most important databases and tools to integrate into this effort?
+
*# Interoperability group 2 (EvoD-EvoD): Develop a plan for interoperability among EvoDs, and with other community resources through alignment, considering the types of driving research questions (similarity searches on function, homology, etc.).  What are the most important databases and tools to integrate into this effort?
 
* 2:45-3:15 Group reports
 
* 2:45-3:15 Group reports
 
* 3:15 Coffee break
 
* 3:15 Coffee break
Line 81: Line 79:
 
== Reading ==
 
== Reading ==
  
* We have started to 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.
+
* Within the Phenoscape project, we have been tagging interesting references about phenotype and taxonomy ontologies by using 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, 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]
 
# 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.
+
# 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.-->
 +
 
 +
== Final report ==
 +
* The [[Media:Phenotype_mtgreport.pdf|final report]] from this workshop summarizes the participants views as the specific research questions to be answered and thus goals to be achieved through a community‐based grant.  Break-out groups provided perspective on the questions below.
 +
1. What are the key gaps in tools to develop your work?
 +
2. What are key obstacles to data exchange and data integration?
 +
3. What do you perceive as the key ontologies that are lacking?
 +
4. What are the gaps in expertise in understanding, developing and applying
 +
ontologies in the community?
  
 
== Participants ==
 
== Participants ==
  
Members of the project team are in '''bold font'''.
+
Members of Phenoscape are in '''bold font'''.
  
 
{| border="1" cellpadding="3" cellspacing="0"
 
{| border="1" cellpadding="3" cellspacing="0"
 
|-
 
|-
 
! Name !! Institution
 
! Name !! Institution
{{EventParticipant|Blake|Judy|Judith.Blake@jax.org|The Jackson Lab|''}}
+
{{EventParticipant|Blake|Judy|Judith%2eBlake%40jax%2eorg|The Jackson Laboratory |}}
{{EventParticipant|Coddington|Jonathan|CODDINGTON@si.edu|Department of Entomology, Smithsonian Institution|'''}}
+
{{EventParticipant|Coddington|Jonathan|CODDINGTON%40si%2eedu|Department of Entomology, Smithsonian Institution|}}
{{EventParticipant|Cowell|Lindsey|lgcowell@duke.edu|Duke University Medical Center|'''}}
+
{{EventParticipant|Cowell|Lindsay|lgcowell%40duke%2eedu|Duke University Medical Center |}}
{{EventParticipant|Deans|Andy|andy_deans@ncsu.edu|NESCent|'''}}
+
{{EventParticipant|Deans|Andy|andy_deans%40ncsu%2eedu|Hymenoptera Tree of Life and Department of Entomology, North Carolina State University|}}
{{EventParticipant|Dumont|Betsy|bdumont@bio.umass.edu|Department of Biology, Univerity of Massachusetts, Amherst|'''}}
+
{{EventParticipant|Dumont|Betsy|bdumont%40bio%2eumass%2eedu|Department of Biology, Univerity of Massachusetts, Amherst|}}
{{EventParticipant|Huala|Eva|huala@acoma.stanford.edu|The Arabidopsis Information Resource|'''}}
+
{{EventParticipant|Huala|Eva|huala%40acoma%2estanford%2eedu|The Arabidopsis Information Resource|}}
{{EventParticipant|Lapp|Hilmar|hlapp%40nescent%2eorg|NESCent|'''}}
+
{{EventParticipant|Lapp|Hilmar|hlapp%40nescent%2eorg|Phenoscape and NESCent|'''}}
{{EventParticipant|Lewis|Suzi|suzi@berkeleybop.org|Berkeley Bioinformatics and Ontology Project |'''}}
+
{{EventParticipant|Lewis|Suzi|suzi%40berkeleybop%2eorg|Berkeley Bioinformatics and Ontology Project |}}
{{EventParticipant|Maglia|Anne|magliaa@mst.edu|Missouri University of Science and Technology|'''}}
+
{{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|Phenoscape and Department of Biology, University of South Dakota|'''}}
{{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|University of South Dakota|'''}}
+
{{EventParticipant|Maglia|Anne|magliaa%40mst%2eedu|Missouri University of Science and Technology|}}
{{EventParticipant|Midford|Peter|petermidford%40yahoo%2ecom|Dept. of Ecology and Evolutionary Biology, University of Kansas|'''}}
+
{{EventParticipant|Mast|Austin|amast%40bio%2efsu%2eedu|Florida State University|}}
{{EventParticipant|Parr|Cyndy|csparr@gmail.com |Smithsonian Institution and Encyclopedia of Life|'''}}
+
{{EventParticipant|Midford|Peter|peter%2emidford%40gmail%2ecom| Phenoscape and Dept. of Ecology and Evolutionary Biology, University of Kansas|'''}}
{{EventParticipant|Riccardi|Grey|riccardi@ci.fsu.edu|College of Information, Florida State University|'''}}
+
{{EventParticipant|Parr|Cyndy|csparr%40gmail%2ecom |Smithsonian Institution and Encyclopedia of Life|}}
{{EventParticipant|Sereno|Paul|dinosaur@uchicago.edu|University of Chicago|'''}}
+
{{EventParticipant|Riccardi|Greg|riccardi%40ci%2efsu%2eedu|College of Information, Florida State University|}}
{{EventParticipant|Stoltzfus|Arlin|Stoltzfus|Center for Advanced Research in Biotechnology|'''}}
+
{{EventParticipant|Sereno|Paul|dinosaur%40uchicago%2eedu|University of Chicago|}}
{{EventParticipant|Vision|Todd|tjv%40bio%2eunc%2eedu|NESCent, and Department of Biology, University of North Carolina at Chapel Hill|'''}}
+
{{EventParticipant|Stoltzfus|Arlin|stoltzfu%40umbi%2eumd%2eedu|Center for Advanced Research in Biotechnology, University of Maryland|}}
{{EventParticipant|Vize|Peter|pvize@ucalgary.ca|Department of Biology, University of Calgary|'''}}
+
{{EventParticipant|Vision|Todd|tjv%40bio%2eunc%2eedu|Phenoscape, 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|Vize|Peter|pvize%40ucalgary%2eca|Department of Biology, University of Calgary|}}
 +
{{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu| Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon |'''}}
 
|}
 
|}
  

Latest revision as of 02:21, 21 February 2011

Phenotype Ontology Coordination Workshop: April 27-28, 2009

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 27-28, 2009

Organizers: Paula Mabee, Monte Westerfield, Todd Vision

Introduction

The goal of this workshop is to discuss plans for an RCN (Research Coordination Network) or INTEROP (Community-based Data Interoperability Networks) application to NSF that we would submit in July or August 2009. The grant would provide funds for 3-5 years of meetings and workshops (and in the case of the INTEROP program, implementation to a limited extent) to identify problems and develop methods and plans to describe phenotypes in a much broader range of species.

Specific goals are to be determined by the workshop participants. An initial list includes establishing and maintaining communication among evolutionary biologists and model organism communities developing ontologies, coordinating efforts among the broader ontology community so that these ontologies are interoperable, and methods to align and reason across multi-species ontologies for phenotype and taxonomy. The workshop includes interested members from both the model organism and evolutionary biology communities.

Agenda

Monday, Apr. 27, 2009

Taking stock: Where do we stand? What resources and needs do we have in common? Identify broader community needs for a [Comparative Evolutionary] Phenotype Consortium that are not currently served by individual grants.

Morning: What new ontologies are required? How do existing common ontologies need to be extended?

  • 8:00 SHUTTLE FROM HOTEL
  • 8:15 Coffee & pastries
  • 8:30-9:30 Welcomes from NESCent (Todd Vision) and participant introductions (2-3 minute lightening talks)
  • 9:30-9:45 Paula Mabee: Introduction
  • 9:45 Breakout groups (4 groups, all 4 questions each):
  • Breakout questions: Tools (software), standards, and ontologies
  • 1. What are the key gaps in tools to develop your work?
  • 2. What are key obstacles to data exchange and data integration?
  • 3. What do you perceive as the key ontologies that are lacking?
  • 4. What are the gaps in expertise in understanding, developing and applying ontologies in the community?
  • 10:45 Coffee
  • 11:00-11:45 Second breakout (2 groups, 2 questions each)
  • 11:45-12:15 Reports from break-out groups
  • 12:15 LUNCH

Afternoon: Annotation and Interoperability

  • 1:30 – 2:00: Case study and analysis; interoperability (Monte Westerfield)
  • 2:00 – 2:45: Breakout groups:
    1. Annotation group: What phenotype curation/annotation needs are there that are not adequately met? E.g. software, standards, best-practices, education, syntax, etc.
    2. Interoperability group 1 (MOD-EvoD): Develop a plan for interoperability between MODs and EvoDs through ontology synchronization and alignment
    3. Interoperability group 2 (EvoD-EvoD): Develop a plan for interoperability among EvoDs, and with other community resources through alignment, considering the types of driving research questions (similarity searches on function, homology, etc.). What are the most important databases and tools to integrate into this effort?
  • 2:45-3:15 Group reports
  • 3:15 Coffee break
  • 3:30-4:15: Annotation, Interoperability I and II break out groups (different participants)
  • 4:15-5:00: Reports from break outs and discussion
  • 5:00: Van back to hotel
  • 5:30-6:30: Drinks at hotel
  • 6:30 Van from hotel to dinner (whole group)

Tuesday, Apr. 27, 2009

Morning: Databases and Trees;

  • 8:00 SHUTTLE FROM HOTEL
  • 8:15 Coffee & pastries
  • 8:45 – 9:30 Break out groups
    1. Database group: Do we have database needs for annotations from this grant activity? Common database, i.e. a vision to create a community resource for comparative phenotype data?
    2. Tree group: How does phylogenetic tree inference vs. mapping intersect with the needs of a phenotype consortium?
    3. Outreach group: What are the priority outreach elements from this grant? How to make these ontologies and annotations (?) available to the broader community? Training (e.g. summer course at Biosynthesis Center, CSH, NESCent, NCESC? Other?); Develop online tutorials? Infrastructure for basics: mailing list, meeting announcements, etc.
  • 9:30-10:00 Reports from break out groups
  • 10:00-10:15 Coffee
  • 10:15-10:30: Decisions on who will write up break out group ideas
  • 10:30-11:30: Writing
  • 11:30-12:00: Action items, plans, preliminary coordination of grant proposal
  • 12:00 Lunch, participants leave

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

  • Within the Phenoscape project, we have been tagging interesting references about phenotype and taxonomy ontologies by using the tag "phenoscape" on Connotea. Everyone is welcome to suggest references by using this tag.

Final report

  • The final report from this workshop summarizes the participants views as the specific research questions to be answered and thus goals to be achieved through a community‐based grant. Break-out groups provided perspective on the questions below.

1. What are the key gaps in tools to develop your work? 2. What are key obstacles to data exchange and data integration? 3. What do you perceive as the key ontologies that are lacking? 4. What are the gaps in expertise in understanding, developing and applying ontologies in the community?

Participants

Members of Phenoscape are in bold font.

Name Institution
Judy Blake The Jackson Laboratory
Jonathan Coddington Department of Entomology, Smithsonian Institution
Lindsay Cowell Duke University Medical Center
Andy Deans Hymenoptera Tree of Life and Department of Entomology, North Carolina State University
Betsy Dumont Department of Biology, Univerity of Massachusetts, Amherst
Eva Huala The Arabidopsis Information Resource
Hilmar Lapp Phenoscape and NESCent
Suzi Lewis Berkeley Bioinformatics and Ontology Project
Paula Mabee Phenoscape and Department of Biology, University of South Dakota
Anne Maglia Missouri University of Science and Technology
Austin Mast Florida State University
Peter Midford Phenoscape and Dept. of Ecology and Evolutionary Biology, University of Kansas
Cyndy Parr Smithsonian Institution and Encyclopedia of Life
Greg Riccardi College of Information, Florida State University
Paul Sereno University of Chicago
Arlin Stoltzfus Center for Advanced Research in Biotechnology, University of Maryland
Todd Vision Phenoscape, NESCent, and Department of Biology, University of North Carolina at Chapel Hill
Peter Vize Department of Biology, University of Calgary
Monte Westerfield Phenoscape, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon