GO Reference Genome Meeting: Difference between revisions
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Discussion points: | 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? | # 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 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? | # 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? | # 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: | Papers of Interest: | ||
Line 48: | Line 52: | ||
# 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. | # 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. | # Wapinski, I., Pfeffer, A., Friedman, N., and Regew, A. 2007. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23:1549-1558. | ||
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====Afternoon of the 26th ==== | ====Afternoon of the 26th ==== | ||
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* Metrics - Moderator Ruth Lovering | * Metrics - Moderator Ruth Lovering | ||
* Tools - Moderator: Chris Mungall | * Tools - Moderator: Chris Mungall | ||
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====Morning of the 27th ==== | ====Morning of the 27th ==== | ||
* annotation consistency | * annotation consistency | ||
* promotion of resource | * promotion of resource |
Revision as of 22:18, 11 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
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:
- 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.
Afternoon of the 26th
* Priorities - Moderators Rex Chisholm and Pascal Gaudet * Methods - * Metrics - Moderator Ruth Lovering * Tools - Moderator: Chris Mungall
Morning of the 27th
* annotation consistency * promotion of resource