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
  • Investigate verification check issues on a fresh install
  • Ability to switch between incremental reasoning on/off states. - In Progress

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.


    • 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

  • Prioritize tracker items
  • Follow OBO-Edit on Twitter!


  • new DBxref verification check requested by Susan Tweedie
    • Can we instigate a check for DBxrefs of the form ID:0. A number of these have slipped though in GO recently. They cause problems for chado loading.

Ticket here: https://sourceforge.net/tracker/?func=detail&aid=2800022&group_id=36855&atid=418260

  • Features that would be useful to have for Buffalo workshop:
    • A way to convert intersection differentia to relations when saving implied links. See ticket:

save implied links misfeature - https://sourceforge.net/tracker/index.php?func=detail&aid=2305594&group_id=36855&atid=418257

    • A system for saving appropriate subsets of terms from one ontology for reasoning in another:

See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260. Details of how this could work require some discussion.

  • Request for info (DS): I would like a practical guide to how GO are managing XPs and instantiating links implied using them

At the Buffalo workshop, I'd like to present both GO and FBbt approaches to working with XPs.

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

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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