Reference Genome Annotation Meeting
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The first Reference Genome annotation Meeting will be held September 26-27, 2007 in Princeton, NJ, right after the GO consortium and GO advisors meeting.
Karen E: Metrics
- Metrics are required to measure own annotation progress. We will use both functional and structural information in these metrics.
- Karen: Structural sequence annotations by comparison of the GFF3 provided by the reference genome groups.
- Each reference genome must provide its sequence as GFF3 file. View table of the reference genome MODs GFF3
- Chris: Review of our progress to date by examining what is actually in the database
- Suzi: Discussion of additional metrics and their consistent use
Judy: 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
Michael: How to prioritize genes
- Rex and Pascale: By Disease
- Currently (): 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?
- Suzi: Discuss pathways as an alternative method of prioritizing genes
Chris: Review of progress toward database and tool development
- Chris, Sohel and Mary are developing a web-based tool that will replace the current Google spreadsheet
- Demonstration of the tool (link to a page with the tool coming soon)
- Curator input for further development
Pascale: Annotation consistency discussion
- How to assess the progress made towards curation of reference genome genes
- strategies for improvement
Rex: Outreach possibilities
- Write a paper describing the reference genome effort. Right now we have >200 genes annotated
- Contact NCBI to ask them to add reference genomes tags onto GenBank records
- see also [wiki]