RefGenome07Aug07 Phone Conference (Archived)

Present

Petra Fey (dictyBase)
Pascale Gaudet (dictyBase)
Karen Christie (SGD)
Ruth Lovering (HGNC)
Judy Blake (MGI)
David Hill (MGI)
Harold Drabkin (MGI)
Mary Dolan (MGI)
Emily Dimmer (GOA)
Kimberly Van Auken (wormbase)
Donghui Li(TAIR)
Susan Tweedie (flybase)
Val Wood (Sanger- pombe)
Victoria Petri (RGD)
Chris Mungall (NCBO)

Review Action Items

Tuesday August 7, 2007, 10 AM CDT (8 AM PDT, 4 PM BST)

Judy, Petra, Karen, DongHui and Kimberley summarize how the different Tools for identifying orthologs work, algorithm explanations, order of preference and pitfalls in identifying orthologs

Judy recommended reading Alexeyenko, Lindberg, Perez-Bercoff and Sonnhammer (2006) Overview and comparison of ortholog datavases. Drug Discovery Today: Technologies, 3: 137.

Annotation consistency/ quality control: Rex and Pascale will send all the curators on the RG mailing list a list of genes to verify; we'll see how it goes and discuss next time. See example ATPAF2
Continue discussion on Outreach: publicizing the project and developing a web presence (lead by Susan and Rex)
Continue discussion on Metrics: breath and depth of annotations (Rex, Judy, Ruth)

Not done; let's do it prior to the next meeting to be able to discuss it at the reference gebome meeting at the end of September.

Curation QC

example: ATPAF2
The idea is each curator (or a small group of curators) could generate a page like this when curating a gene; other groups could consult the page when curating the ortholog from their database
Very heated discussion about the usefulness of ISS annotations in the ref genome annotation effort.
Judy: To expand a little bit more on my take on the relationship between ISS and the RefGenome Project.

The Ref Genome Project is to provide comprehensive annotations for high priority genes. These annotations would then be useful for emerging genomes who would be able to jump start their genome annotation pipeline through the use of ISS annotations to the experimental data in a closely related taxon.

Note that for the emerging genomes, they would not be making use of the ISS annotations in the MOD file.

So we can look at the ISS annotations as more part of the MOD annotation strategy than as an objective of the Reference Genome Project.

Of course, as a curator is working on a gene, one works both from the Ref Genome perspective but also as a curator for the particular MOD group, and the curator would probably want to add appropriate ISS as they proceeded.

Pascale: the goal of that page was not about ISS (those are more visible than they should have been); it was to have an example of how one curator could have a look at all publications and annotations and comment.

Curation Targets

We have now shared a spreadsheet where curators can make suggestions for targets

[[1]]

RGD (Mary Shimoyama) sent two lists: one of neurological and cardiovascular diseases (692 genes); the other with genes associated with obesity (1222 genes)
How should we proceed to select new targets? We decided to chose from the neurological diseases. Pascale, Emily, Ruth will select targets for September.

Reference genome curation tool

RG software group and some curators had a phone conference to discuss the new tool
Sohel has made a new version of the interface

http://rails-dev.bioinformatics.northwestern.edu:24000/

Keep sending comments

Reference_Genome_Database_Requirements_Discussion; however since Sohel leaves July 31, development will be delayed

How to interact with AmiGO

Next meeting

Tuesday Sept 11, 1 PM CDT (11 AM PDT, 7 PM BST)