Phenotype Ontology Coordination Workshop
**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:
- 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 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
- 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?
- Tree group: How does phylogenetic tree inference vs. mapping
intersect with the needs of a phenotype consortium?
- 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 |
|——|——————————–|