AHWG-20090519

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Present

Rama, Seth, Amelia, Ben, Jane

Time

~20 min.

Agenda

A more serious discussion of the next AmiGO release: 1.7. And more immediately, I'd like to gauge how tired the working group is from testing because I think it might be a good idea to have a point release (code changed) that includes the addition of Google Analytics code; and would incidentally include code that standardizes how graphs are displayed, which is where the bulk of the testing would come in.

Another option would be to wait until we have a more finished release, but that would mean losing all of the potential user information from AmiGO until then. Upside, less of the testing. There are other options for how to do this as well.

Resources for general 1.7 stuff:

http://wiki.geneontology.org/index.php/AmiGO_1_7

https://sourceforge.net/tracker/?group_id=36855&atid=494390

Val made a couple of suggestions which I thought we could discuss:

  1. It would be really nice to have a summary page for the slimmer with only the total numbers of genes annotated to each slim term. The results page is really cumbersome with every gene product lites, and I am guessing that most people really want the numbers. The lsit of genes should be accessible but may be better not on the main page (or the option to get a results summary output instead of a long output)?
  2. have a default that if you select an organism, but do not provide an input gene list, it slims the entire gene set for the organism. I am guessing that many users would like to see the GO slim for their organism without the added hassle of obtaining a redundent gene list in the correct format.

I think they're both good ideas.

Also, I really, really think we need to figure out how we will incorporate IEAs, at least for the Term Enrichment tool.

The DB filter for the TE tool is still deeply confusing (uses cryptic DB abbs, UniProt v/s UniProt KB still appears) - lets talk about how we could improve in 1.7.

Finally, can we make it so the GO slimmer allows you to upload your own GA file?

[Jane]

Discussion

  • Should we push out a quick release for analytics (and incidentally the graphing)?
    • Everybody seems to approve.
  • People should look at the tracker for items for 1.7.
  • Discussed important points from software group meeting.
    • IEAs going in
    • work on species
  • Jane covered Val's points above.

Action Items

  • Seth will get the next release ready and talk to the WPWG next week.
  • Seth will add Val's points to the tracker.

Previous and Ongoing Action Items

  • web converter for old-format obo files (part of general purpose converter).
  • action item (chris) to remind ev code group
  • release SOP wishlist (seth)
    • then ask ben
  • discuss SOP when we have more people
  • send notes along to software group
    • amigo data structs (amelia)
    • ref gen and DBIx::Class (seth)
  • put all new stuff in next release tracker (seth)
  • clean tracker more
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