Manager 15August2012

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Agenda

GO helpdesk JIRA set-up

Can we come to a decision wrt the archive so we can move forward on this please? The GO helpers were relaxed about having the archive live outside of JIRA.

Action: Rama to look into retiring Stanford go-help email list: 1. 'Vacation message' when you email the list, 2. will the archive remain searchable if the list is retired?

GPAD format

We discussed earlier this year adding an explicit relationship in the annotation format between the gp and the GO term. The plan would be for this to supersede the contributes_to, colocalizes_with and NOT qualifier column in the current GAF. We were trying to figure out default relationships for legacy annotations, and I think this was where we stalled?

Anyway, Becky, Brenley and I have been working on finishing the virus terms, and one of the prerequisites of being able to annotate with these terms is that you are able to specify whether the gp originates from the organism that plays the host or the symbiont (viral) role in the process, so we need a relationship to be able to do this (originates_from_host/symbiont?)

Looking at the GPAD format doc:

http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format

It seems that additional relationships are allowed in the qualifier column. So do we accept GPAD files yet? And if so, would we want to just allow an additional qualifier or do we want to fully specify this column, retrofitting relationships for all terms?

Action: Jane to further specify host/symbiont relations

Action: Chris to oversee migration of annotation files to svn

Quarterly report

Where are we on this? What are the dates for the next quarter? Can we decide what our aims are for it at this meeting (or make it an action for the next?)

Action: PIs to come up with a mechanism to generate and follow-up quarterly aims