Managers 10Oct07: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 7: Line 7:


== Review Action Items from previous meeting ==
== Review Action Items from previous meeting ==
*Display replaced_by & consider tags in AmiGO (Chris/swug): Chris: you can see this in AmiGO already although the way it's done needs to be cleaned [DONE]
*Display replaced_by & consider tags in AmiGO (Chris/swug)  
DONE, Chris: you can see this in AmiGO already although the way it's done needs to be cleaned  
*Finish & submit NAR update (Midori)  
*Finish & submit NAR update (Midori)  
DONE, accepted
DONE, accepted

Revision as of 11:35, 10 October 2007

GO Managers, Weds. Oct. 10 8 AM PDT / 10 AM CDT / 11 AM EDT / 4 PM BST

Agenda/chair: Midori
Minutes: Pascale
Present: Chris, Midori, Jen, Pascale, Judy, David

Review Action Items from previous meeting

  • Display replaced_by & consider tags in AmiGO (Chris/swug)

DONE, Chris: you can see this in AmiGO already although the way it's done needs to be cleaned

  • Finish & submit NAR update (Midori)

DONE, accepted

  • Several meeting preparation tasks - reports, wiki additions, etc. (all managers)

DONE, obviously

Individual Manager reports

Ontology Development

Outreach

Software

Reference Genomes

User Advocacy

Meetings

Collaborations and Interactions, active and new

Operations and Procedures

Staffing and Personnel

John has been Googled!!

Budget issues

Publications

  • NAR manuscript accepted!
  • Current Protocols in Bioinformatics article update (Judy & Midori)

Other Current Topics and Concerns

  • Specific items (with relevant management groups):

Annotation: Do we want to encourage submission of annotations of alternate spliceforms?

Judy summaries: the ref genome group is aware that the annotation of multiple splice forms can pose problems: - we need to know which product we are annotating and we need to know which gene this belongs to

- Do we need another column?

- Chris: at the RefG meeting we talked about using a mapping, similar to the gp2protein file, which can have a one-to-many relationship

- Chris: can I have a feel for how many groups do it? MGI (structured notes), rat, who?

- Suzi: would everyone NEED to to it?

- Judy, no

- Chris: we can make a proposal: two ways of doing it: for eg, if MGI has two splice variants, they use the gene ID, and if they know the splice variant, they include that in the structured note; the other way is like UniProt, which maps all back to the 'parent' gene. UniProt also uses s suffix (people dont really like to encode information in the ID)

- two options: add splice variant ID in gene_id column of in new column

- Suzi prefers the first option because it seems 'cleaner'; annotate to the actual product having activity; however several issues with that (), so generally option 2 is favored

- Suzi: does that also include non-gene things like ESTs?

-David: that rises an interesting point: if there is an unpublished variant

[ACTION ITEM]: Chris will write a proposal for how to deal with this (including adding a new column?)

Microarray annotations

- Chris: we do not allow more granular annotation?

- Pascale: isn't that dealt with in column 12 or so? and use SO terms there

- Yes but everyone has 'gene' there

- Should we not be annotating to gene products? yes, but most people do not do it yet

- Midori: we hadn't decided which part of SO we can use

-Suzi: I thought all SO terms were allowed (that made sense in that context)

- Suzi: back to microRNAs: there is the gene, the transcript, and the gene product (processed transcript)

- David: how does the SO treat the miRNAs?

- All gene products are grouped by functional categories; for mRNAs, is the SO talking about the pre-miRNA or the processed miRNA?

- Chris: I think they are both represented. If the SO needs to be fixed we'll do it.

- David: also, the miRNA field is changing really fast [ACTION ITEM]: Think about updating documentation to state that all terms from SO are accepted. Chris: we need to do this with the splice variants.