OEWG 20110621

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OBO-Edit Working Group Meeting: Tuesday, June 21, 2011, 8:30am PDT

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

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi Harris, Paola Roncaglia, Midori Harris, Marcus Chibucos, Laurel Cooper, Karen Christie, Heiko Dietze, Chris Mungall

Bug and Feature Trackers

Fixed since last meeting

  • Problem Running in Windows 7
    • This bug has been reported multiple times, e.g. Unable to start oboedit 2.1.3 windows version
    • The workaround is to choose a lower memory allocation than the one suggested by the installer. Alyona (the latest user to complain) confirmed that this worked for her.
    • I added a note about this to the text on the installer page that asks you to set the memory. (Not that people will actually read it, but at least we can then point it out to them when they complain.) I also added a note to the Configuration Manager page in the user guide.
    • There is no actual fix for this problem--Windows just doesn't seem to be able to launch Java applications with the amount of memory the installer thinks should work. There is no way to change that in this installer-builder software.
  • Bad handling of unrecognized relation (text editor et al.)
    • Unrecognized relation was shown wrong or misleadingly in many components, including Ontology Tree Editor (the unrecognized relation didn't show up under 'Relations', and the child didn't appear under the parent to which it is linked with the unrecognized relation), Parent Editor (unrecognized relation shown as "is_a"), and more.
    • Chris said it was ok to add a new OBOProperty for the unrecognized relation (rather than a dangling property object, which is not treated the same by OE). The newly-created relation name is "name (UNDECLARED)", so it should be clear to the user. (They also get a warning message during load--and in fact they can't even load a file with an undefined relation unless they have checked off 'Allow dangling' in the advanced load interface.)
  • Don't save dbxref lib description to obo file

Currently working on

  • Is_a closure broken
    • Filtered save with "is_a closure" checked not saving the right terms.
    • There are still issues with this
  • filtered save doesn't save dangling parents
    • David wrote: "A filter specifies a bunch of term stanzas to save, some of which may have relationships whose objects are not in saved stanzas. 'Allow dangling references' should save those relationships. In 2.1beta3, it does. In 2.1beta13 and 2.1beta14 it does not. Not sure what beta was the first to have this bug."
    • David's example works for Midori in b14 (and for me in all the OE versions I tested, including b12 and b7)--maybe David needs to get rid of his oboedit_config?
  • Ancestor/descendant relationships missing
    • In the search panel, when looking for descendants/ancestors of a term, the pulldown menu for relationships only includes default obo-edit relationships and not ontology-specific relationships.
  • child search ignores relationship type

Next bugs to work on

  • problems with assert implied links panel
    • The Assert Implied Links panel behaves badly in various ways. Will not be trivial to fix.
  • equivalent_to cycle not detected
    • OE is not complaining about an equivalent_to cycle when it should (discussion on PATO mailing list).
    • I'm not sure whether there's already a verification check that should be checking this, or whether I'll need to create a new verification check.


  • No spaces in dbxrefs -- Since there aren't supposed to be any spaces in dbxrefs, it would be helpful if there were an error message (fatal error?) when a space was included in a dbxref.
    • There is already a warning message about this, though it's a bit cryptic--it says "Dbxref of [term] contains non-URI characters (such as >)". If others want me to make this a fatal error rather than just a warning, I can do that. (Also let me know if you have suggestions for the wording of that warning.)
  • Assert Implied Links problems
    • Nomi will look into these and try to assess how hard they would be to fix.
    • Midori mentioned that the Remove Redundant Links panel has similar problems--e.g., problem with select all.
    • Chris said that the two components have shared or similar code, and it would make sense to fix the Assert Implied Links problems first. That might fix some of the Remove Redundant Links problems at the same time, or at least make it clear how to address them.
  • When I click "Add as def dbxref" in the Dbxref Library, it works; however, "Add dbxref" does nothing. I also tried it with "Apply to all selected terms" checked off, which didn't help. I tried an old OBO-Edit and got the same behavior. Is this a (not yet reported) bug, or am I doing something wrong?
    • Midori replied: "Add dbxref" works in b1 and b4, but not in b7 or anything since then (I don't have b5 or b6 handy).
    • Nomi added this as a bug report (but obviously it's not high priority, since no one mentioned it before)
  • Next OEWG meetings:
    • Next meeting will be July 5th
    • Nomi will be away July 19; however, she will be in Cambridge/Hinxton visiting some OEWG members on July 21 and 22. Should we have an OEWG meeting on July 21 or 22 (8:30am PDT or thereabouts)? Nomi will set up a Doodle poll.
    • Nomi will also be away August 2--we'll just skip that one.
  • is_a closure problems: Marcus sent an example, including PDF of what he's seeing, to the OEWG mailing list. Nomi is looking into it.


Back to OEWG meeting agenda and minutes list