2008-10 SAB Meeting

Logistics

Instructions_for_Registration

Agenda

User Advocacy - Ashburner

Key accomplishments

• AmiGO 1.6
• GOOSE? (Have they seen this already?)
• Help desk report
• Newsletter

Annotation - Cherry

Aims and Key accomplishments

• Good annotation outreach efforts have been organized by AgBase, TAIR and PAMGO.
• Annotation camps
• Annotation IRC
• Evidence Code Ontology

Questions for SAB

• How can we get support for someone to take on the stewardship of the Evidince Code Ontology? (e.g. addition of HTP for ref. genome)
• Due to the lack of available funding, no new annotation groups have been added in this recent period. It is proving to be very difficult for other species database groups to find funding for GO curators.
  

Our current approaches to work round this are:

• • 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?

Ontology Development - Blake

Aims and Key accomplishments

• Ontology Quality control Logic-based cross-product definitions

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

• The regulates relationships have been incorporated into the biological process (BP) ontology.
• Changes stemming from two content meetings have gone live
  • Cardiovascular physiology/development
  • Muscle Development
• Sensu terms renamed and rationalized
• New OBO-Edit features (video)

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 (e.g.) bacterial sequencing centers want to use them to facilitate annotation. We also know that they will be valuable when users cluster annotations that have only been annotated to the MF ontology. Can the SAB think of additional use cases?
• What is the best way to present new relationship types, such as has_part and regulates, to users? Should searches include or exclude them by default, should we offer users the choice, or try to make everything work somehow behind the scenes? Relationship composition is also relevant to this question.
• 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.

Reference Genome Annotation Project - Lewis

Aims and Key accomplishments

• Working on methods to establish curation sets (PANTHER, PPOD, Paul Thomas, Kara Dolinski)
• Since the last GOC meeting (and reference genome meeting), put a lot of emphasis on annotation consistency during the monthly conference calls and two electronic jamboree
• Publication submitted (I hope it will be)
• POGO demo

Questions for SAB

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