OEWG 20090310

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OBO-Edit Working Group, Tuesday March 10th, 2008 9.30 a.m. PST

Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425

Agenda/Chair: Jen
Minutes: KarenC
Attendees: Amina, Midori, Harold, Jen, Karen C, David OS, Tanya

Action items carried over

  • Midori
  1. will compose email about OE2 release to be sent out about one week before release, which is March 23rd.
    • not relevant since we're not at this point yet
  • Working Group:
  1. Documentation Jamboree
    • This coming Friday 13th March, everyone please look over the documentation for the section(s) that you tested. Post comments to the wiki.
  • Amina
  1. Option to turn off incremental reasoning
    • in progress
  2. Look into what 'succinct' does and will change documentation on 'succinct' , including what it is called.
  3. GraphViewer should not need the reasoner to show asserted links. Since this is a new feature for OE2, should not hold up the release. Could just label as experimental. DavidOS suggests that 'succinct' be the default because the output with succinct on makes sense while with it off, the result is gibberish.
    • This item is on Amina's to do list. In response to the suggestion that perhaps the Graph Viewer should just be considered experimental, Amina responded that she feels that this component is mostly working well, shouldn't be too hard to fix, and should not be considered experimental. From beta56 onwards, asserted links will not require the reasoner.
  4. Investigate why uncommitted text edit window shows up without edits having been done.
    • Fix in progress.
  5. Restore load error report before release (from Melissa) https://sourceforge.net/tracker/index.php?func=detail&aid=2513220&group_id=36855&atid=418257
    • This is in progress
  6. (Look into open source java help documentation software. Can be after release. For now, WG members can email docs to Amina and she will integrate into the code.
    • Taking off action item list, to be looked into after the release

Tracker items to be reviewed by the Working Group

  1. Edit layout does not work on windows https://sourceforge.net/tracker2/?func=detail&aid=2657452&group_id=36855&atid=418257
    • proposal to have a way to go back to the default settings for both the edit and verify layouts
  2. Bug from David: When you click on a search result item, it takes a while for the text editor to catch up, or maybe takes a double click. Seems a common problem, though not everyone has seen it. https://sourceforge.net/tracker2/?func=detail&aid=2588958&group_id=36855&atid=418257
    • The problem is that he gets an empty list with the reasoner on
  3. Bug from David - See https://sourceforge.net/tracker/index.php?func=detail&aid=2637233&group_id=36855&atid=418257
    • Rearrangements of tree editor during save, others see this too. Linkpile reasoner thinks there is a disjoint problem, gets confused, and jumps around. A Long log file showing the reasoner going around and around. Amina added some better descriptors to log file to help with this sort of issue.
    • Crashing in b55 when saving with reasoner on, wasn't happening in b54. Maybe we can try incremental reasoning? Checkbox in reasoner manager?
    • False disjoint relation issue in flyanat, Chris says that incremental reasoning is not working correctly.
    • The option to turn off incremental reasoning is already in progress. The rest will go on Amina's to do list.
  4. Bug from Midori- see https://sourceforge.net/tracker/index.php?func=detail&aid=2642262&group_id=36855&atid=418257 can't delete "general" dbxrefs in the term editor- Amina has fixed this in b56.
    • no need to discuss since already fixed in upcoming beta56

Discussion items

  1. b56 release
    • expect this to come out on Friday or on Monday of next week
  2. Jen - A computer scientist friend of mine called Satnam Singh (Microsoft Research, Cambridge) is possibly interested to collaborate on speeding up incremental reasoning in OBO-Edit. Would you be happy for me to go ahead and explain the problem to him, to see if he is interested to pursue this further? This collaboration might also present an avenue for solving my current funding problem, as the reserch institute has a funding programme specifically to support this kind of collaboration (http://research.microsoft.com/en-us/groups/rpp/). Clearly there would have to be very solid agreements about the work remaining open source, and in the public domain, but I could discuss this aspect with him and report back.
    • There was unanimity that any such collaboration absolutely must not change the free, open source license for OBO-Edit. People were OK with Jen doing research to determine the details of such a collaboration. Following through would require the go ahead from Chris as well as from the GO PIs. There is already an item about this on tomorrow's managers meeting call.
  3. Consider/replaced_by: it turned out to be a hassle to get a 'copy to clipboard' button on a dialog box. How would it be best to present the information for users?(Jen) Message.jpg
    • It was suggested that having this check be part of the verification checks might solve the issue of having the list be in a window from which it is difficult to copy/paste. Jen will look into this.
  4. Where should we store small test ontologies, like the one that I have made for testing obsoletion? Maybe in cvs somewhere? (Jen)
    • There is already a place in cvs for test resources.
  5. Do we want to test Clackpoint VoIP? It means the Mac people need to install Flash 10 so it may be best to wait until this arrives on its own. (Jen)
    • A test occurred after the meeting. Jen sent an email to the working group email list requesting feedback.

Non-agenda items

  1. Was there resolution for the Windows user who was having problems?
    • Jen has set up a meeting with him for the morning of Wed March 11th
  2. David reports that the Harvard group of Flybase is having trouble loading some of the GO and anatomy files. The problem seems to be due to problem characters in the Description field from the definition dbxref manager. Various people noted that this is not the first time that this has been a problem. It was suggested that while the Description is really useful when using the dbxref manager, it is not necessary for the book titles, etc., to go into the obo file itself.
    • David will submit a feature request proposing this change.
  3. David also reported that the Harvard group is having problems with undesired loading of the regulates relationship. Having just received the report from Harvard, it isn't completely clear what the problem is.
    • David will look into it further to determine the exact nature of the relationship loading issue for FlyBase Harvard.

New Action Items


  1. will work on way to return to default settings for both the edit and verify layouts (https://sourceforge.net/tracker2/?func=detail&aid=2657452&group_id=36855&atid=418257)
  2. will add these bugs to her to do list:


  1. will find out whether it is possible to collaborte with or accept funding from Microsoft Research without affecting the free open source status of OBO-Edit, and will also discuss it at the GO managers' meeting tomorrow March 11th.
  2. will look into whether a verification check for obsolete terms referred to in consider and replace by tags will serve the purpose of making the list easy to obtain


  1. David will submit a feature request proposing that the Description field of the definition dbxref manager is no longer inserted into the saved file.
  2. David will look into it further to determine the exact nature of the relationship loading issue for FlyBase Harvard.


  1. Documentation jam on Friday March 13th. Everyone should look at the documentation for the sections they tested and other sections as well if possible and add comments to the wiki.


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