Managers 10Oct07

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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)
  • Finish & submit NAR update (Midori)

DONE

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-David: that rises an interesting point: if there is an unpublished variant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