RefG Bar Harbor May 20-21 2010
Agenda
May 20th, morning
Introduction
- 8:15 - 8:45 Arrive: coffee
- Rm ERB 2535
- 8:45 - 9:00 Welcome: Judy
- Introductions
- 9:00 - 9:30 Overview: Pascale
- Description of the rationale and strategy for carrying out integrated biocuration projects
(see http://gocwiki.geneontology.org/index.php/Strategy_for_establishing_RefG_annotation_priorities)
How the GO represents lung branching morphogenesis
- 11:30 - 12:15 David
- Will include live review of GO structure
Seminar: Zena Werb
- 10:30 - 11:30
- CC Little Auditorium
- '"Of mice and women: How studying mammary development gives us insights into breast cancer"
Rationale for target selection
- 9:30 - 10;15 Target Selection: Carol
- Review of basic biology involved in branching morphogenesis, specifically in the lung. .
- Why/How was this particular set of genes chosen?
- How do the selected targets relate to one another biologically? (viz. a diagram showing their relationships to one another)
Question from Mike L.: How do we interpret lung-specific annotations when it comes to propagating annotations to zebrafish?
Lunch 12:15 - 1:30 Roscoe's
May 20th, afternoon
Status of the completed MOD experiment-based annotations
1:30 - 2:15 Li, wiki pages
Mike
Possible topics for discussion:
- Topology issues for FOXF1 (AN812) and FOXI (AN619) clades
- No lung-specific cilium terms. E.G.: GO:0042384 "cilium assembly" has a "sensory" child, but no lung, airway, epithelium, etc child. Possible issue for Foxj1. May also be an issue for gut cilia.
- Choosing structured notes vs. specific GO terms: several SF items.
- Can the notes be used in PAINT?
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=2997217&group_id=36855 . Should we use a lung-specific child term or an "in lung" note on the parental term?
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=2998363&group_id=36855
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=3000642&group_id=36855
- Scope of propagation: the FoxC1/C2 clade
May 21th, morning
PTHR10159
Pascale
Li
May 21th, afternoon
Summary
Paul
- If this process is to be effective then what changes and improvements do we need to make?
- File structure must be simpler for MODs to import (ie, not one GAF per family - but concatenate one file per MOD)
- New evidence codes must be accepted
- References must be publicly available
- It must be clear what data each MOD needs to import
- Reach out beyond MODs for importing PAINT-generated GAF files
Preparatory materials
Background reading
- PMID 18463632
- PMID 16613830
- PMID 17237346
Attendees
from away
- Pascale Gaudet
- Suzi Lewis
- Mike Livstone
- Paul Thomas
- Chris Mungall
- Rama Balakrishnan
- Hernan Espinoza [Krasnow lab]
- Arjun Guha [Cardoso lab]
local
- Li Ni
- Judy Blake
- Carol Bult
- David Hill
- Mary Dolan
- Randy Babiuk
others from Jax have been invited to attend as they wish.