SWUG:Meeting 2007-08-22

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Meeting notes

Present: Chris, Suzi, Amelia, Mary, John, Ben, Dan, plus special guests David and Richard from the EBI

Absent: Stan, Seth

Review of previous action items

  • Documentation : Chris, Seth and Amelia to redirect links
  • ID Tracking : Chris, Mary to send RQs to Stan
  • Protein family annotation tool : Suzi to send
 cut from grant
  • Ben to add tests for graph loading issues
  • Seth and Amelia will write something for the newsletter.
  • Loading orthology into main database

Reports and Discussion

Software Architecture, Schema and Modeling

  • ID mapping

ACTION: Dan will create mapping files

  • Cross-ontology linkages

Discussed implications for database loading in particular graph_path filling. Plan: Use the OBO-Edit code for building path table in future.

ACTION: Chris will write document

  • Versioning

no time to discuss. Document available:



  • Interface stuff. redesigned OE filtering interface.
  • Autocomplete for java swing


  • Session, query overhaul

Reference Genomes

  • Mary redid refG graphs, added symbols
  • Comparison table based on GO slim
  • Mary Started on installing database in order to integrate displays
  • RoR code still at DictyBase


  • bulkloading : on hold until sequence loading stuff done
  • new release of GOA
  • EBI MySQL mirror was broken due to update script, now fixed.

Stan wasn't present, but sent this in an email after:

  • sequence loading: rewrite (to speed up retrieval and loading protein sequences) finished but unreleased (together with the rewrite of amigo loading).
  • gp2protein report:
    • the report script has contacted mods for issues identified from gp2protein file
    • mods replied and updated/explained the issues: wb, gramene, zfin, sgd
    • mods replied and are looking into the issues: tair, fb, tigr
    • make reports available on-line: unresolved go cvs user privilege issue at stanford
  • ID mapping: pending RQs from mary and chris.

Documentation & Outreach, Papers, Presentations

  • Progress Report (last 6 months)
  • GOC & Advisors Meeting preparation
  • NAR preparation (last 2 years)


Review of Action Items