OEWG 20111101

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OBO-Edit Working Group Meeting: Tuesday, November 1, 2011, 8:30am PDT

NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Saving Time. (The EU has also gone off Summer Time, so any European participants also need to call an hour earlier than usual.)

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Attendees: Nomi, Midori, Heiko, Harold, Paola, Chris M.

Bug and Feature Trackers

Fixed since last meeting

  • definition dbxref button not working
    • I thought I had fixed this in b19 but it mysteriously stopped working again in rc1.
  • Dictionary errors when adding to alwayslowercase
    • Note that this was not a new bug; this had been in OE for a long time and probably hadn't been noticed because the quick fixes weren't working.
  • At Chris M's request, these adapters or components (and their user guide pages) have been removed:
    • The OBO OWL Adapter
    • The OWL URL Reader
    • The GO Association File Adapter
    • Semantic Parser Manager
  • Chris M. noted a few things in the user guide that need to be updated. I have fixed these (and a few more), but there are definitely still some out-of-date sections. If you notice any that are particularly egregious, let me know.


  • 2.1-rc2 released 10/14; many downloads.
    • Windows most popular platform by far (surprisingly)
  • Information from one term is lost during merge
    • I was unable to reproduce this problem; however, I did come across a null pointer exception that sometimes happened during a merge, and which could potentially have caused merge problems. I have fixed this.
    • Jane (who reported the problem) said that removing her oboedit_config/perspectives didn't fix the merge problem, but then the merge problem spontaneously went away and the merge now works for her.
    • If anyone else observes this problem, please let me know. The specific case where Jane observed the problem was with gene_ontology_ext.obo, trying to merge GO:0019282 into GO:0003961.
  • If no new bugs are reported in the next week, 2.1-rc3 will be released as official release 2.1.
    • I have asked Mike Cherry and the GO group to test it in their pipeline (twice), but have gotten no response. Can someone in GO help move this along?
    • Someone suggested asking Karen Christie. (Done.)
  • Filtered save demo and discussion of how to use filtered save to create a slim ontology--not this time. Someone will do this next time if there's interest.

Currently working on

  • Working towards making an official 2.1 release

Next bugs to work on


Back to OEWG meeting agenda and minutes list