SWUG:Meeting 2007-05-30

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Agenda Notes

Sohel can't make it this week, so we won't be having an in-depth discussion of refgenomes - Mary will give us an update.

Dan - I have volunteered you for SWUG outreach - can you check the emails to the software-group from gohelp and make sure everything has been answered adequately & is in the FAQ?

Present at meeting

Chris, Gail, Amelia, John, Mary, Seth

Agenda Preamble

This will be our regular meeting time, every 2 weeks. I realise it's not ideal for everyone, Stan won't be able to consistently make it. But it's the best that can be done given our constraints. Let's try it for a while; we can try an alternating slot later in the year.


Review of previous action items

  • ACTION: documentation
    • Finally done. Will review.
  • ACTION: discuss time for reg meetings

    • Ben will probably have to cut out at 9:45 (but not today)
  • ACTION: Suzi is to send out description of requirements for protein family annotation tool and see if anyone is interested in working on this
    • Whiff.
  • ISSUE: Identifier tracking. Matching ref. genome ids to MOD ids. Stan says that EBI has a tool we might be able to use.
    • Stan sent an interpro mapping file but we are not sure if this is what we need or if it's the same as gp2protein.
    • TODO Set up a phone call with Chris, Stan, Ben, Sohel, Mary to discuss this.
  • ACTION: Chris & Mary are to send requirements to this list.
    • On wiki
  • ACTION: Chris, Seth, and Amelia to document GO-dev by next meeting and rest of group will critique then.
    • Done?
  • ACTION: Amelia will be moving GO FAQ to wiki pages.
    • Done

Reports and Discussion

OBO-Edit (John)

  • 2.0 beta release
    • installer won't work, need CVS?
  • plans
    • many internal arch. changes
    • new bulk intersection editor
    • graph-based editing (draw it!) - integrated with reasoner
    • graph-based DAG viewer - replaces tree view
    • not finished state - more features will be added:
      • flex doc library (drag-and-drop interface)
      • reasoner improvement
    • auto-complete components added to library (is anyone using it)
    • reasoner great for x-products (chebi, etc.)
  • Amelia wants to know about search algorithms for AmiGO.

AmiGO (Amelia)

  • latest changes
  • release in June/July -
    • rewritten search to make it efficient.
    • return results in a more intuitive way
    • "special intelligence" - tries selected fields first, then other fields
  • does this use go-dbi API? by-passed, but not in templates
    • relevance score does fractions of terms in match
    • might not be efficient to use John's algorithm
    • AmiGO feature meeting?
  • (Seth)
    • Is Amigo 2.0 a re-write of amigo 1.0 code, or we will reuse?
      • We will reuse and replace piecemeal.
  • Integrate term finder and mapper for June/July release

ORB (Seth)

  • service for obo foundry.org - makes term requests simple.
  • cgi-client currently + arbitrary xml clients.
  • set up on toy server - will send URL
  • Reference Genomes (Mary)

- Requirements

Discussion on the wiki - ensuring consistent use of identifiers. Sohel looking at use cases curators have to enter genes, keep track of curation.

- schema changes - integrating visualisation with AmiGO

Ref geneome graphs - interactive tool.

  • Documentation & Outreach (Dan)

- EBI & ensembl mirror - documentation - gohelp emails

Mirroring script to capture older versions of database - seth to look at.

  • Production Databases (Ben)

Working on loading slowly. Next project is getting fully taxonomy data.

  • Software Architecture (Chris)

- db presentation

  • Papers

John submitting paper on graph-based editing. draft of amigo paper (Seth) ready to