OEWG 20100316

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OBO-Edit Working Group, Tuesday March 16th, 2010 8.30 a.m. PDT

Conference call details: New GOC conference call numbers
US: 1 866 953 9688
UK: 0808 238 6001
pin: 801561

Agenda/Chair: Amina
Minutes: Midori
Attendees: Amina, Midori, Terry, Ramona, Karen, Harold, Jane, DavidOS, Chris

Action items carried over

Bug and Feature Tracker Updates


Discussion items

Terry - is_a closure a little funky (using GO and Cell ontology in XPs)

  • describes symptoms
    • saves ancestral terms but doesn't save term of interest
    • no is_a relationship associated with ancestral GO terms
    • loses differentiae

Amina - supposed to save relationships

Terry will put in bug report.

Later, Chris joins and replicates is_a closure thing.

Terry also getting out-of-memory errors.

Ramona - not saving properly; not saving definitions, etc. for new terms.

  • opened version of plant ontology; added term with definition, etc.; loses definition upon changing selection (autocommit on) or saving file

Amina - delete configuration folder if you see problems after installing new beta.

Amina working on refactoring text editor and other components; will see if save issue is related.

Dictionary should be fixed now on Mac ... but Harold still has same problem saving to user.dict. Checks and finds that terms are being saved now, but OE ignores the new entries.

Amina helps Ramona find log file to send ...

Harold - has tried to recreate his crashing problem; it seems to be better now.

Jane & David - "uncommitted text edits" problem worse than ever (David has updated existing bug report). Amina will fix soon (connected with text editor revamp).

David reports some "really weird stuff", including the bug report above. Very odd, dangerous things happening, such as unexpected new genera or tags. More details in bug report. Amina will try to replicate; gets suggestions from David for what to try.

Chris tries demo for bug -- there's a new option, "create new genus-diff child", so one possibility is that selection isn't sensitive enough - choosing wrong menu option

more discussion of this bug and verification implications ... add request for verification check: can't have exactly one intersection_of tags (can haze zero or two or more).

David - can we create some test files? (small ontology files to use for testing)

Chris and david checking logs ...

David - has anyone else had problem with roots not syncing (i.e. text editor, etc. not updating upon root selection)? Most of us haven't tried it; Terry tries and doesn't have a problem (he has reasoner off; problem is with reasoner on). Some discussion between David & Amina ...

(some is_a closure discussion that your well-meaning minute-taker didn't completely catch)

David & Chris describe correct is_a closure behavior

some chat about script that follows is_a paths to roots - David will email to Amina et al.

Discussion of reported minor (but disconcerting) bug where xp edits are committed, but look like they aren't. Chris demos to try to replicate it. More discussion ensues.

Warning: Don't use parent editor to delete intersection parent in 2.1-beta3.

  • Pending Items and Fixes Coming up

Action Items

  • add request for verification check: can't have exactly one intersection_of tags (can haze zero or two or more) (Davidos or Chris?)
  • Amina - update tracker items
  • Jane will submit bug report about text edits failing to commit
  • next wg meeting maybe in 1 week - will be announced to the list


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