2008-10 SAB Meeting

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October 2008 Meeting Logistics


Ontology Development - Blake

Aims and Key accomplishments

Progress reported at current GOC meeting, plus items reported at SLC GOC meeting (April):

Also see Progress Reports from April and October 2008.

Questions for SAB

  • We are committed to creating links between MF and BP, and know that it will facilitate annotation.
    • Initially we plan to work on area XY ; does that make sense and are there other suggestions?
  • Update on metrics: Are the metrics for ontology development that we now provide useful? What additional metrics should we gather, and how? Are we getting better at providing metrics? And (off on a bit of a tangent) are there any use cases for metrics other than our internal monitoring, SAB reporting, and funding agency reporting (not that we'd stop measuring if there aren't!)?
  • Essentially the same questions about quality control measures - are our existing QC practices good; what others can we add; etc.
  • Are we getting ontology content submissions/suggestions from a broad enough segment of our users? If not, which other groups (or even individuals) should we target? How can we motivate them to get involved?
  • Maybe: ask SAB the questions about content development priorities on GOC meeting agenda.

User Advocacy - Ashburner

Key accomplishments

  • AmiGO 1.6
  • Help desk report
  • Newsletter

Questions for SAB

Annotation - Cherry

Aims and Key accomplishments

  • Good annotation outreach efforts have been organized by AgBase, TAIR and PAMGO.
  • Changes to GAF
  • Annotation camps
  • Annotation IRC
  • Evidence Code Ontology
  • Swiss-Prot committed to start doing GO annotation which will help getting more gene proteins annotated, including proteins from species not currently being annotated. (4 Slides from Jennifer to explain why other organisms also need to be annotated, leading in to Michael's talk on SwissProt.)

Questions for SAB

To help other groups annotate:

  • Write better documentation to enable small community groups and individual users to make anntotations. (Docs by Reference Genome Group.)
  • Work on making the GO structure more intuitive for users so that when community annotation is made, it is more likely to be accurate. (Ontology Development Group)

Do the SAB see any other approaches that might be better?

Reference Genome Annotation Project - Lewis

Aims and Key accomplishments

  • Publication submitted (I hope it will be)
  • Paul Thomas: gp2protein files issues; (link wiki page describing what we need to generate a proper gp2protein file) Chris/Stan/Paul to provide numerical profiles.
  • Working on methods to establish curation sets (PANTHER, PPOD, Paul Thomas, Kara Dolinski).
  • Pascale Gaudet: Development of shared GO curation guidelines that are being adopted by all ref. genome MODs. Since the last GOC meeting (and reference genome meeting), put a lot of emphasis on annotation consistency.
    • Monthly conference calls
    • two electronic jamboree
  • Suzi Lewis: TCT demo and proposed data flow

Questions for SAB

  1. How do we obtain compliance in generating these protein files?
  2. How do we obtain compliance in adhering to curation guidelines?
  3. Annotation consistency : do we need evidences codes other than EXP, NON-EXP and IEA? This is one major cause for inconsistent annotations.

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