OEWG 20120103

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OBO-Edit Working Group Meeting: Tuesday, January 3, 2012, 8:30am PST

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

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Chris M., Heiko, Karen, Laurel, Midori, Becky, Paola, Ramona

Bug and Feature Trackers


  • Released version 2.1.0. Release 2.1.1 will come soon.
    • The main reason for getting release 2.1.0 out (even though 2.1.1 is coming soon) is so that GO editors, who are required to use a non-beta version, can switch to using 2.1.0 now rather than having to save everything in OE 2.0 as well.
      • Karen C. will check with Mike Cherry to get his official approval for switching to 2.1.0. (He already tested 2.1-rc3 in the pipeline and verified that it's good.)
  • Harold thought that the latest version seemed to start up slower than the previous release candidate a few weeks ago. I'm not aware of any reason why this should happen--has anyone else observed this?
    • Becky and Paola also found the initial startup to be a tad slower. Nomi will investigate.
      • Later: my tests show the startup time to be the same (it prints how long it takes to start up, so I'm not just going by my subjective impression).
      • You could try moving your oboedit_config to see if that helps.
      • You didn't add any new filters or anything, right?
  • Can't save cross products (in OE1 or OE2)
    • Some users said that when they created cross products, in OE, they weren't getting saved properly. Alex wrote, "I also made a few cross products today -- or one the wrong genus term got saved, for another no genus term got saved." However, he could not find a repeatable example of this problem.
    • I tested cross-product creation and at first it seemed to me that there was a bug--the genus you saved would sometimes convert to a different one. But it turned out that what was happening was that the autocomplete dropdown for the genus field offers you synonyms as well as term names, but if you choose one that happens to be a synonym, the cross product editor silently converts that to the primary term name, since there isn't a term with the name you selected. That may not be desirable behavior, but it's not actually a bug--the changed genus is not just random.
    • I was unable to find any other examples where the cross-product editor lost or messed up the genus name. If there are other cases where it misbehaves, I need examples.
    • I have made the behavior easier to understand by implementing a requested feature: Show IDs as well as term name/synonym in the Genus box
    • Can I close this bug report?
  • Can't delete genus in cross product tab
    • I implemented a genus trashcan, but unfortunately it didn't work properly in Autocommit mode so I had to comment it out for release 2.1.0. I hope to get it working for 2.1.1.
    • As before, you can use the Parent Editor to delete an unwanted genus.
  • Updated some user guide pages:
    • Changed documentation on how to hide disjoint_from links in the Graph Editor (do it using the Graph Editor filtering, NOT with a global link filter).
      • Chris M. said that he is recommending a new disjoint_from strategy: instead of including disjoint_from links in the main ontology file, store them in a separate file and load only when needed to validate the ontology. (He will explain this to GO editors at the upcoming workshop, Jan 30-31.) If you follow this strategy, then you don't need to worry about disjoint_from "hairballs" in the Graph Editor.
    • Updated page on creating cross products in the Text Editor.
    • Added Ramona's text about how to specify the domain and range of a relation.
  • Since the GO workshop is coming up at the end of the month (January 30-31), we agreed to have another OEWG meeting in two weeks (Jan 17).

Fixed since last meeting

Currently working on

  • For some reason, the version number in the installed version is coming out as 2.1 instead of 2.1.0; I'm trying to fix that.

Next bugs/feature requests to work on

  • Chris and Heiko will get OBO<->OWL conversion working inside OE
  • Automatic detection of changed files/reload option
    • OE will check whether the file you're looking at has changed on disk since you last loaded or saved it
      • May be too complicated to implement for multiple files
    • Karen (I think) noted that when you load a file, say foo.obo, and then edit it and save it as, say, bar.obo, the OE titlebar still says foo.obo. Would be nice if the title would change to the saved filename.
      • Nomi will look into this. (Later: I got this working.)
    • cvs revision tag check Jane requested, "Can OE look at the cvs revision in the header of the file to see that the file it's saving over is the same as the one it loaded? And if not, give a warning. We occasionally lose changes this way if we cvs update before saving in OE - OE writes over the patched file when the save is then made."
      • This is a special case of checking whether the file has changed on disk, and will be covered by that (but OE will not specifically check cvs revision information)
  • Can't delete genus in cross product tab
    • Need to get genus trashcan working in Autocommit mode


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