GO Reference Genome Meeting: Difference between revisions
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* promotion of resource | * promotion of resource | ||
====Annotation Consistency | ====Annotation Consistency ==== | ||
Moderator: Pascale Gaudet | |||
====Promotion of Resource (moderator Susan Tweedie)==== | ====Promotion of Resource (moderator Susan Tweedie)==== |
Revision as of 07:50, 12 September 2007
Sept 26-27th, 2007 Princeton, New Jersey
Wednesday, September 26, 2007
- Meeting Location: Frist Campus Center - Multipurpose Room C
- Lunch Meal Location: Frist Campus Center - Food Gallery
- Coffee/Tea/Water service for 30 people during the morning and afternoon sessions
- Lunch - $8.50/person on meal cards to be used in the Food Gallery
- Dinner - TBA
Thursday, September 27, 2007
- Meeting Location: Frist Campus Center - Multipurpose Room B
- Lunch Meal Location: Frist Campus Center - Food Gallery
- Coffee/Tea/Water service for 25 people during the morning and afternoon sessions
- Lunch - $8.50/person on meal cards to be used in the Food Gallery
- Dinner - TBA
Agenda Details, Discusstions and Topics
High Level Topics Identified for Discussion
- Strategies to identify orthologs
- How to prioritize disease genes
- How to assess the progress made towards curation of reference genome genes; strategies for improvement
- Discussions regarding metrics, including making a plan for how to use metrics
- Review of progress toward database and tool development
- Annotation consistency discussion
- Outreach
Schedule (last updated September 10, 2007)
Morning of the 26th
* orthology * GRIN (Genome Research Informatics Network) conference call tentatively 11 am
Orthology
Moderator: Kara Dolinski
Resources:
- The Reference Genome groups have provided descriptions of their current methodology for establishing orthologs for their gene sets. These are available on the Orthology discussion page.
Discussion points:
- Is it necessary for all groups to use the same methodology in order to create orthology/homology data sets for the reference genome project?
- Standardize/describe procedure for identification across MODs
- How stringent and consistent do we want the language of 'orthology' and 'homology' to be incorporated into our documentation and discussion?
- How will we update our orthology sets with new genome builds or do we consider the current genomes in the reference genome project to be essentially complete?
- What is the impact of closely-related paralogs that have different functions on this project?
- Which model organisms are available in which databases, e.g. Dicty is not in Treefam; zebra fish & chicken are not in YOGY
- use-case examples (Kimberley wormbase, also Donghui?)
- Emily: GOA discussion about inheriting annotations
Papers of Interest:
- Alexeyenko, A., Lindberg, J., Perez-Bercoff, A., and Sonnhammer E.L.L. 2006. Overview and comparison of ortholog databases. Drug Discovery Today: Technologies 3:137-143.
- Dolinski, K. and Botstein, D. 2007. Orthology and Functional Conservation in Eukaryotes. Annu. Rev. Genet. 41:463-507.
- Hulsen, T., Huynen, M.A., de Vlieg, J., and Groenen, P.M.A. 2007. Benchmarking ortholog identification methods using functional genomics data. Genome Biology 7:R31.
- Wapinski, I., Pfeffer, A., Friedman, N., and Regew, A. 2007. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23:1549-1558.
GRIN conference call
Afternoon of the 26th
* Priorities - Moderators Rex Chisholm and Pascal Gaudet * Methods - * Metrics - Moderator Ruth Lovering * Tools - Moderator: Chris Mungall
Priorities
How to prioritize disease genes
- Currently (Rex and Pascale): OMIM morbid map; also occasionally we find genes not in Morbid Map that have strong evidence for involvement in a disease
- There is an effort to cluster genes involved in the same disease or with the same or
related function to facilitate the curatorial effort
- Questions: is there a more systematic way? should we target some diseases more specifically? What about multigene diseases ?
Methods
Metrics
Moderator: Ruth Lovering
Ruth provided this stating point http://gocwiki.geneontology.org/index.php/Metrics:_breath_and_depth_of_annotations
Tools
Moderator: Chris Mungall
Topics
- Database: moving out of Google spreadsheet
Morning of the 27th
* annotation consistency * promotion of resource
Annotation Consistency
Moderator: Pascale Gaudet