OEWG 20110125

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OBO-Edit Working Group, Tuesday January 25th, 2011 8.30 a.m. PST

Conference call details: New GOC conference call numbers
US: 1 866 953 9688
UK: 0808 238 6001
pin: 801561

Agenda/Chair: Nomi Harris
Minutes: Midori
Attendees: Nomi, Midori, Ramona, Becky, Terry, Marcus, Harold

Action items carried over

Bug and Feature Tracker Updates

Discussion items


  • Release 2.1b8 available
    • How frequently should I make releases?
      • Consensus that we can wait for more or bigger bug fixes, but somewhat more frequent than Amina did would be welcome. Nomi will ask
    • Should this version become the official release 2.1 (assuming it behaves ok when tested), or should I try to fix more bugs first?
      • Several people agree that it's fine as is for the editing tasks they're doing. Also see below on bugs.
  • Updates to OEWG membership?
    • Inclined to err on inclusive side for mailing list. Nomi will email list to remind members how to unsubscribe if they want.
  • I have looked at and updated most of the open bug reports that have priorities >5, and am starting to look at the high-priority feature requests as well.

Fixed since last meeting:

  • User dictionary now works
  • Text Editor commit problems fixed
    • In the past (e.g., in OE-2.000), after you added a new synonym and clicked Commit, the synonym editor (with a place to add a Name and Xrefs) changed back to the synonym display, showing the synonym name with the Scope under it and (if the synonym was in red) the little fixer tool icon. In 2.1-b7, nothing visibly changed when you click commit--the synonym editor stayed open rather than changing to the synonym display, so it looked like the edit wasn't committed. I have fixed this.
      • Harold reports that it now works for him. Nomi reports a bit detail on an outstanding bit of the problem connected with loading an ontology that contains the same term as edited in previous load/edit session.
    • Fixing this also turned out to fix Harold's problem, where an out-of-date perspective was making his Text Editor erroneously claim that there were uncommitted edits. (However, keep in mind that because perspectives are serialized binary files, they can get out of synch with newer OBO-Edit versions. If you are experiencing new problems with OE, it's always worth trying the experiment of renaming your config directory (and letting OE create a new one) and seeing if that helps.)
  • Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
    • Thanks, Chris!
    • Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.

Next bugs to work on:

  • Bad handling of unrecognized relation (text editor et al.)
    • This is now the only priority-8 bug. Is this the most important bug for me to tackle next?
      • Probably not; it's not easy to tell how big a fix it would take. Priority setting depends on what you count - could be a big problem if encountered, but in practice unlikely to affect many, at least in the wg. Probably ok to lower priority.
  • Obsolete terms appear in Discriminating relations. Questions:
    • Should I make ALL autofill suggestions exclude obsolete terms? That should be doable. Otherwise, it's going to be tricky, because the autofill code doesn't know what the term is going to be used for.
      • Yes; everyone likes this idea.
    • This bug report also mentions a feature request that's come up before: please show the namespace each term belongs to. This feature may be more important than it used to be because more people are working with multiple ontologies (which may contain duplicate terms).
      • Is this a high-priority feature?
      • As indicated in a reply to this feature request, the terms can be colored by namespace by constructing a term renderer in the Global Filters interface. Would someone like to volunteer to write up instructions on how to do that, and I'll add it to the user guide? (We could even make that behavior the default, if people like the idea.)
      • Agree that new feature isn't a high priority. Terry will write up instructions on setting up renderers.
  • obomerge doesn't report definition clashes:
    • obomerge doesn't even attempt to check clashes between definitions or other fields, other than IDs. Should it? How high-priority is that? How many people are actively using obomerge?
      • GO editors use it occasionally, but always in conjunction with a diff utility, so GO doesn't have a presing need for obomerge to detect text edit clashes. Nobody else at meeting does eiher. Lower priority; and it's more a feature request than bug.
  • Some disjoint_from relationships impossible to delete
    • This works for me--can someone else test it and confirm that it's fixed?
      • Nobody else has done the kind of work that would run into this problem.
  • ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago). How important is this?
    • Most wg members don't even know what it does! Nomi will bring it up with Chris.
  • Other high-priority bugs? (Bump up their priorities in the tracker, if needed.)
    • Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
    • Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quetting/etc.

Issues raised in meeting

  • Ramona's problem launching 2.1beta8 traced to java version: she has 1.5, but OE needs 1.6. Nomi will help Ramona install Java 1.6.
  • Ramona has custom relations, and their icons have disappeared. She'll put in a bug report.
  • Becky put in bug report on autocomplete selection. Sounds familiar to several of us. Nomi will look at it.



Action Items

  • Nomi will email wg mailing list to remind members how to unsubscribe if they want.
  • Terry will write instructions on how to use renderers to color terms by namespaces. Nomi will add to the user guide.
  • Ramona will submit bug report on disappearing relation icons.
  • Nomi will add note about reasoner & memory to user guide.
  • Nomi will look at autocomplete selection bug again.


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