RCN Meeting, 23-25 February 2012

 

Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species.
Paula Mabee, Andrew Deans, Eva Huala, Suzanna E Lewis
Stand. Genomic Sci. 2012 6:3



Presentations

RCN Introduction (Paula Mabee)
Introduction to Ontologies (Gary Merrill)
Introduction to Anatomy ontologies (Melissa Haendel)
The PATO ontology (George Gkoutos)
Phenotype annotation and representation (Jim Balhoff)
Reasoning and ontologies (Sue Rhee)
Reasoning and ontologies (Chris Mungall)
Human disease (Monte Westerfield)
Phenoscape (Paula Mabee)
Biodiversity (Andy Deans)

Working Group meeting summaries


Phenotype RCN meeting agenda
23-25 February 2012
National Evolutionary Synthesis Center, Durham, NC

Thursday, Feb. 23, 2012
8:00 am: Shuttle to NESCent from Marriott
8:15: Continental breakfast at NESCent
8:45 – 9:30: Introductions and welcome from NESCent and RCN PIs
9:30 – 10:30: Introduction to Ontologies (Gary Merrill)
10:30 – 10:45: Coffee break
10:45 – 11:15: Introduction to Anatomy ontologies (Melissa Haendel)
11:15 – 12:45: Hands-on exercises:
• Natural language annotation exercise
• Anatomy ontology building exercise
12:45: LUNCH
2:00 – 2:30: Phenotype annotation and representation (Jim Balhoff)
2:30 – 3:00: The PATO ontology (George Gkoutos)
3:00: Hands-on annotation exercise (small groups)
4:15: Coffee break
4:45: Annotation outcome (Jim Balhoff)
5:00: Panel discussion (Suzanna Lewis): What are the challenges?
6:00: Shuttle back to hotel
7:00: Dinner

Friday, Feb. 24, 2012
8:00 am: Shuttle to NESCent from Marriott
8:15: Continental breakfast at NESCent (upstairs)
9:00: Reasoning and ontologies (Sue Rhee)
9:30: Reasoning and ontologies (Chris Mungall)
10:00: Examples of reasoning: Human disease (Monte Westerfield); Phenoscape (Paula Mabee); Biodiversity (Andy Deans)
10:30: Coffee break
11:00: Problem-focused breakout groups
12:30 pm: LUNCH; Advisory Board meeting
2:30: Birds of a feather breakout groups
4:00: Coffee break
4:30: Report-out from breakout groups
5:00: Cocktail hour
6:00: Shuttle back to hotel
7:00: Group Dinner at Pop’s

Saturday, Feb. 25, 2012
8:00 am: Shuttle to NESCent from Marriott
8:15: Continental breakfast at NESCent
9:00 – 10:30: Next steps & Collaborative breakout groups
10:30 – 11:00: Coffee break
11:00: Synthesis and discussion
12:00 pm: Meeting ends; Airport shuttles


The main focus of this meeting was to introduce and establish communication between scientists from several different research backgrounds including comparative evolutionary biologists, model organism biologists, applied scientists, and ontology developers and logicians. We introduced concepts involved in developing and coordinating ontologies as well as ontology annotation.

Phenotype RCN PIs:

Paula Mabee (pmabee@usd.edu)
Eva Huala (huala@acoma.stanford.edu)
Andy Deans (andy_deans@ncsu.edu)
Suzanna Lewis (suzi@berkeleybop.org)