Phenotype Ontology Coordination Workshop

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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


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.


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?

  • 8:15 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;

  • 8:15 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


  • 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)


  • 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?


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