OEWG 20110405

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OBO-Edit Working Group Meeting: Tuesday, April 5, 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 Christie, Laurel Cooper, Marcus Chibucos, Midori Harris, Paola Roncaglia, Rebecca Foulger

Bug and Feature Tracker Updates

Discussion items

From last meeting

  • Trying to help Paola to get her OBO-Edit behaving like Becky's. Problems with her dictionary. None of her problems appear to be OBO-Edit bugs.
    • Paola got it working. She wrote, "The problem seemed to be with the way the dict files were transmitted/copied over. Emailing, zipping or loading/downloading from web repository did not work, but simply copying the files on a memory stick did the trick."
  • Someone asked whether there's a way to see the most recently modified items in the SourceForge bug tracker. There isn't a way to sort by Last Modified, but this query will show you tracker items (bug or feature) that were modified in 2011 and that are still open.
  • Ramona would like to be able to move undocked windows behind other windows instead of being in front of everything. (The user guide window can do this.)
    • Unfortunately, this is not really doable, because the component window stuff is handled by a third-party package (infonode.docking) and it appears that undocked--aka floating--windows are DEFINED as floating in front of the other components, and this behavior is not configurable. OE's user guide window is different because it is created as a new window by a different method (and it can't be docked--it's not a dockable component).

Fixed since last meeting

  • explanation component not working
    • The Explanations component and Graph Editor weren't showing explanations for some newer explanation types (just the question, "Why is this link in the ontology?"). Now they show raw explanations for any explanation types that don't have a pretty form defined. This fix was deemed good enough.
  • When you use the magnifying glass in the user guide, you get duplicate items, and one of the duplicates is empty and the other has the info.
    • I remembered having fixed this before (others agreed). I discovered that Amina disabled my fix last year for some reason. I have re-fixed it.
    • This fix just affects the building of the user guide index, so if it broke anything, it would only affect that.
  • Chris added a new simple reasoner called "DirectLinkReasoner". It can only infer "direct" links, whereas the other reasoner does more.
    • Direct links are typically trivial inferences that are useful for working in OBO-Edit:
      • infer a simple link from an intersection link
      • infer symmetric class-level axioms (e.g. X disjoint_from Y <-> Y disjoint_from X)
    • Use of this reasoner may possibly introduce a slight impact in responsiveness in OE, compared to running with no reasoner. However, this should be constant (i.e., it should be no worse on an ontology of 10,000 terms compared to an ontology of 10 terms). Brief tests indicate that this decrease in responsiveness is not really noticeable.

Currently working on

  • Configuration manager not opening (on Laurel's Linux box)
    • Works for her on Windows. Works for Nomi on her Linux box (Ubuntu).
    • Nomi requested more information to help track this down.
  • Is_a closure broken
    • Filtered save with "is_a closure" checked doesn't save all the terms it should.
    • Fix in progress
  • parent/child search problem in 2.1-b11
    • In 2.1-b11, selecting 'Parent' or 'Child' in the aspect box makes the search panel stop working. The Self/Root/Parent/Child selector blanks out, and hitting the 'Search' button does nothing.
      • Fixed in 2.1-b12 (coming soon)
    • Note that this bug was new to 2.1-b11 (had to do with trying to disable aspects that don't work right w/o reasoner). However, other related-sounding bugs were co-reported with this one, and they turned out to be old bugs (found in OE versions back to 2.000).
  • Loading multiple ontologies--PATO, GO, cell etc, Marcus gets message "ID profile mismatch--use profile loaded from the file"? Which ontology file is it referring to? It should say which. (Marcus will post this as a bug.)

Next bugs to work on


  • Paola sometimes has to force-quite OBO-Edit (on her Mac). No one else has had this happen. Paola will email Nomi her oboedit log file the next time this happens.
  • New DirectLinkReasoner
    • AI: Some OEWG members (who?) will test the new reasoner before Nomi does the next release.
    • AI: Someone (was it Ramona?) who shared a scenario where the new simple reasoner could be helpful will write up her scenario and send it to Chris and Nomi to make sure it's right; then Nomi will add it to the documentation.
  • AI: Nomi is working with Midori to fix and test the filtered save with is_a closure.
  • AI: Should we disable "child" and "parent" search aspects if the reasoner is off? Fixing those searches might be hard. Would like Chris's input.


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