OEWG 20090602

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OBO-Edit Working Group, Tuesday June 2nd, 2009 9.30 a.m. PST

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

Agenda/Chair: DavidOS
Minutes: Midori

Action items carried over


  • Lock Layout option - Done
  • Fix logging location for OSX in 2.1

Discussion items

  1. Jen - Filtering system in OBO-Edit.
  • My work on cross products and taxon links is badly held back just now by the lack of a good filtered save in OBO-Edit. I'm wondering if the need is great enough that I should start adding this feature even though we are still bug fixing. I have figured out what the interface could look like:

1) Add a new checkbox: 'choose tags to include'


2) When checked, this box calls up an auto-populated list of all the tag types in the file and the user can then choose which tags to include in each file.


  • DOS comment:
  • Chris's comment:
    • Hardcode an option for exporting a file with only {id,intersection_of} tags, as this would be satisfactory for the majority of use cases involving working with xps as separate files. I think this could be implemented fairly easily.
    • Alternative approach is to always namespace links and xp defs, and have the tag filtering done automatically from this. But I think this involves more work on the editors part as they have to ensure all links are correctly namespaced
  • Key question is how many use cases -- enough to justify the programming time & effort?
    • Not sure yet, although DavidOS can envision using it.
  • Known use cases at present:
    • only id and intersection tags
    • everything but intersection tags

more discussion ...

Conclusion: remove 'typedef' from tag list; Jen will look into how hard it would be to implement the general version as mocked up

  • Prioritize tracker items
    • Action item for all wg members: comment on feature requests and bug reports that affect you
  • Follow OBO-Edit on Twitter!


  • Features that would be useful to have for Buffalo workshop:
  • Request for info (DOS): At the Buffalo workshop, I'd like to present both GO and FBbt approaches to working with XPs.
    • I would therefore like a practical guide to how GO are managing XPs and instantiating links implied using them.
      • Much discussion, in which DavidOS explains reasons for these requests; Tanya describes current GO workflow; DavidOS asks whether GO is asserting anything other than is_a links (answer: not at present); David wants to assert more than just is_a links.
  • Conclusions:
    • additional feature request to have 'assert implied links' assert differentiae as well as is_a, perhaps as a configurable option. This should be separate from stripping out intersection tags.
    • second item carried over to next week

Demos/ Tips/ Ticks

  • Ontology Tree Editor - missing/new features now implemented in OBO-Edit2.1
    • Distinction between local and global mode
    • Now implemented in OBO-Edit2 - the much awaited - Lock View feature!
  • Questions/Discussion points
    • Independent sessions for multiple OTE instances
  • Demo notes
    • Clarified a Very Important Point: the little icon for global mode is a globe.
  • Tree editor
    • Lock view is back! (much rejoicing)
      • Amina mentions some implementation details
        • do we want an icon/button in the component menu bar to lock?
        • some discussion; button good but not high priority
  • Reasoner manager - incremental reasoning off by default, and manager has option to activate it
    • discussion and clarifications on behavior (buttons and checkboxes)
    • Amina will demo next week, so wg can hash out actual workflow and desired interface

Q: Do we need to be able to search for synonyms of a specified type or scope?

A: Not very often, so make it a low-priority feature request

Tip of the week

  • If we don't have anything here until the meeting time - the agenda chair can pick one of the attendees and put them on the spot about their favorite tip
  • Suggestions:
    • Editing the ontology through the OTE - workflow - things to take into consideration
  • Query Building/ How To's
    • How do I search for terms with multiple synonym types that have more than one relation with their ancestors?

Action Items

  • UTF8 support
  • OBO-Edit 2.1 release


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