Reference Genome Annotation Meeting: Difference between revisions
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===Strategies to identify orthologs=== | ===Strategies to identify orthologs=== | ||
* Procedures different databases are using can be found on the [[Orthology discussion page]] | * Procedures different databases are using can be found on the [[Orthology discussion page]] | ||
* We'd like to have an expert explain the different tools: how the algorithms work, which is better (if any), what to do in case of disagreement between tools and how to manually find orthologs if the tools fail to give any results | |||
* Standardize procedure for identification across MODs | * Standardize procedure for identification across MODs | ||
* Which model organisms are available in which databases, e.g. Dicty is not in Treefam; zebra fish & chicken are not in YOGY | * 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 | |||
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Revision as of 12:43, 12 June 2007
General Info
The first Reference Genome annotation Meeting will be held (tentatively) September 26-27, 2007 in Princeton, NJ, right after the GO consortium and GO advisors meeting.
Agenda
Strategies to identify orthologs
- Procedures different databases are using can be found on the Orthology discussion page
- We'd like to have an expert explain the different tools: how the algorithms work, which is better (if any), what to do in case of disagreement between tools and how to manually find orthologs if the tools fail to give any results
- Standardize procedure for identification across MODs
- 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
How to prioritize disease genes
How to assess the progress made towards curation of reference genome genes; strategies for improvement
Review of progress toward database and tool development
- Chris, Sohel and Mary are developing a web-based tool that will replace the currant Google spreadsheet
- Demonstration of the tool (link to a page with the tool coming soon)
- Curator input for further development
Discussions regarding metrics, including making a plan for how to use metrics
- Integrating both functional and structural information into the metrics we develop. How are we going to integrate sequence into this pipeline?
- Each reference genome must provide its sequence as GFF3 file [Karen Eilbeck]