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OBO-Edit Working Group, Thursday July 16th, 2009 8.30 a.m. PST
Conference call details:
Outside US: 1-719-867-3417
Attendees: Amina, Midori, Harold, Jen, Jane, David
Action items carried over
- Feature request: Simplify 'save implied links' interface so that it doesn't have different options and behaves as 'save for presentation' currently does.
- see below
- Amina - find out what does realize implied links do? If we don't need it delete
- Feature request: Optional Verification check to check if is_a child has same namespace as parent.
- AI: Jen has had problems showing all ancestors to root with graph editor- needs to investigate further to write bug report.
- Progress on wishlist for Buffalo:
- Add verification check for non-ascii characters.
- This has become important because of changes to OE introduced by Jim Balhoff to allow UTF-8 text to be saved from OE2.
- Fixes this ticket: 2770450 Support for UTF-8 term names needed ASAP Open 2009-04-17
- New ticket for verification check: 2815837 Add Verification check for non ascii Open 2009-07-02
Updated Tracker Items
- parent search ignores relationship type Fixed
- Simplify 'save implied links' comment on tracker
- Quick summary: Amina suggeted that we keep both options, but give them non-cryptic names ('save all links' and 'save trimmed links') and add warning about 'all links'
- some discussion; we don't really need 'save all links'; OE only ever shows trimmed; trimming different with different reasoners, and rule-based reasoner is correct (eventually we'll get rid of linkpile and forwardchaining ...)
- might as well eventually remove 'all links' option (tho Amina will leave it in and add tooltips for now)
- OBO merge doesn't work! Fixed
- OBO-Merge generates null-pointer exception Fixed
- stop panel changes if click on top comment on tracker
- GAZ.obo not displayed correctly in OBOEdit2.0 Fixed
- affects any ontology with disjoint terms - they show as roots
- David - follow-up question about root detection; some terms with part_of but no is_a parent show up as roots. Probably happens if part_of isn't declared transitive in the ontology file.
- Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd DONE
- save implied links misfeature In progress
- some discussion, mainly on what 'realize implied links' does, and how it differs from 'save implied link' - 'realize' converts link to asserted; more confusion over what 'save' does (sounds like 'save' puts link in file flagged as implied, but check this for accuracy, as minute-taker got a bit lost!)
- Version 2.1 finally ready for release after unexpected delays. Final touches and clean ups in progress.
- Includes bug fixes for above SF items
- Amina finishing up "perform is_a closure for xp terms", which addresses David's need for saving terms from one ontology that are used in another ontology (SF 2116798 above)
- Dictionary & verification stuff still to do
- Autosave generating huge backup files; Amina will fix this before release
- aside: DavidOS has successfully restored from autosave. good!
- Sorting enabled on child and parent name columns in Assert Implied Links Component
- Switched to using OBO-Edit2 last week: Victoria Petri
- Several annotators use OE as a browser
- Disjoint violations only caught by Harold's verification system, not others (Midori has the check enabled on reasoner, and Jane & David have tested this)
- discussion of symptoms in detail
- Harold uses fast reasoner; Midori uses rule-based - a clue?
- more testing during meeting ... YES, it's the reasoner!
- discussion of symptoms in detail
- More comments on OTE display with different reasoners, especially if there are disjoint violations (David)
- David: buggy autocomplete behavior somehow connected with mouse-click vs. keyboard
- Demos and more description of symptoms - what's displayed in search box changes (at least for Jen)
- Harold will file bug report about Graphviz & paths (MAH joined call in middle of discussion of problem details)
- Amina: work on problem with rule-based reasoner not running disjoint check
- Amina: work on problem with rule-based reasoner and graph view
- Amina: look into autocomplete behavior bug (David or Jen to reopen tracker item)
- Amina (and other wg members): tracker cleanup - close items addressed in 2.1 release
- WG members test and then close own items