OEWG 20110816

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OBO-Edit Working Group Meeting: Tuesday, August 16, 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, Karen C., Heiko, Chris M., Midori

Bug and Feature Trackers

Fixed since last meeting

  • Heiko fixed the OE installer so that if you have a 64-bit machine, you can allocate more memory to OE and the launcher will use the correct JavaApplicationStub. (Yay! Thanks, Heiko!)
    • This will mitigate the memory issues caused by the Reasoner.
  • Heiko also made the installer suggest a lower memory allocation for Windows users, which should take care of the issue where Windows users were unable to launch OBO-Edit if they allocated the amount of memory suggested by the installer.
  • Alex Diehl figured out how to make GraphViz work in OS X 10.7. Midori added this information to the OE help page about GraphViz
  • beta 16 removing Xref and DBXref information
    • Fixed in b17: OBO-Edit saves xref description for dbxrefs but NOT for definition xrefs.
    • Karen C. said that because b16 doesn't save dbxref descriptions, she can't really use it for production editing, so Nomi said she'll do a b17 release tomorrow that includes the dbxref description fix.

Discussion Items

  • Heiko has a proposed fix for File browser in Mac OBO-Edit doesn't show second hard drive that involves replacing the current file browser (JFileDialog) with a native one (FileDialog) that shows you (on a Mac) all the same things as in your Finder. However, the native file browser only lets you select one file at a time. Is this a problem? Do OE users want to be able to select and load multiple ontology files via the simple Load interface?

On the left is the current file browser; on the right is the native one.

OldFileBrowser.png NewFileBrowser.png

    • If we switch to the native file browser, can still load multiple files by using the Advanced dialog (which I find clunky):


    • Check with Harold (he loads multiple ontologies a lot)
  • Did anyone (other than Midori) get a chance to test obo2obo to make sure my fix for [ geneontology-Bugs-3316815 ] (filtered save doesn't save dangling parents) didn't break anything in obo2obo?
    • Midori found one issue in obo2obo but it turned out to be old and unimportant
    • obo2obo recently stopped printing output about what it's doing--I'm looking into that.
  • Next meeting: we would normally skip the 5th Tuesday (August 30th) and meet next on Tuesday, September 6, but that Tuesday is not good for Nomi. Can we meet on August 30th and skip September 6th?
  • With a new academic year starting, should we revisit the meeting day/time or just keep it as it is?

Currently working on

  • Name Redundancy check doesn't work
    • Jane wrote, "I managed to commit two terms to GO which had identical names to existing terms this week, without the verification plugin objecting."
    • Nomi and Midori both tested the Name Redundancy check and it worked for them.
    • Karen C. said, "I have just checked the Verification Manager settings and the check boxes for "On text commit?, "On save?", and "On manual?" are ticked. However, I don't recall having been warned in either case. I could easily have overlooked the "On save" warning as I become blase about reading those since there are always 30 or so of those, but I did try to skim through and see if there was anything new. However, I do not recall getting a warning when I committed this term."
    • Clarification from Midori: the redundant name warning appears in the Verification Manager but doesn't appear as a popup (I didn't realize it ever did). I will fix that. Are there other warnings that used to appear as popups that now don't? I don't want to make all the warnings popups because that's annoying.
  • Working towards making an official 2.1 release
    • Trying to get JUnit tests working again (for OBO and OBO-Edit) and make sure that current OE behavior is no worse than the behavior of 2.0.
  • Is_a closure broken
    • Terry wrote, "I just used beta14 to do is_a closure on cell.edit.obo with GO and PR. Overall it worked but there were two issues. 1) Non is_a relationships for previously MIREOTED terms were added, leading to a dangling parents error. For example, "regulates" relationships were added to many GO terms that were already in CL. 2nd, all typedefs disappeared."
    • Midori commented, "I can confirm that I get the same thing (or at least something similar) happening with 'regulates' relationships: is_a closure saves some terms that would only be there if it followed at least one 'regulates' link. Curiously, it didn't include all 'regulates' links; the term I used for testing had a regulates link itself that apparently wasn't followed. Specifically, I tested using a nonsense xp in SO, with the GO term 'regulation of polysaccharide metabolic process' in an intersection_of tag. The saved file contained all the is_a ancestors I expected, plus the is_a ancestors of 'polysaccharide metabolic process' -- but it didn't have 'polysaccharide metabolic process' itself. I'm getting typedefs saved if they match the filter, and not if they don't (all are saved if I tick 'always save properties' - that seems to be working fine).
  • obo2obo no longer prints status messages to stdout

Next bugs to work on

  • Fixing JUnit tests for OBO and OBO-Edit
  • Fixing any bugs that the JUnit tests reveal


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