OEWG 20090716: Difference between revisions

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[[Category:OBO-Edit working group]]
OBO-Edit Working Group, Thursday July 16th, 2009 8.30 a.m. PST <br>
OBO-Edit Working Group, Thursday July 16th, 2009 8.30 a.m. PST <br>


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Agenda/Chair: <br>
Agenda/Chair: Amina<br>
Minutes: <br>
Minutes: Midori<br>
Attendees:
Attendees: Amina, Midori, Harold, Jen, Jane, David


==Action items carried over==
==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.
#  Feature request: Simplify 'save implied links' interface so that it doesn't have different options and behaves as 'save for presentation' currently does.
#* [https://sourceforge.net/tracker/?func=detail&aid=2815829&group_id=36855&atid=418260 2815829  Simplify 'save implied links'  Open  2009-07-02]
##see below
 
## Amina - find out what does realize implied links do? If we don't need it delete
# AI: 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.
# 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.
# 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:
## 2116798  [https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260 Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd  Open  2008-09-17]
###see below
## 2305594  [https://sourceforge.net/tracker/?func=detail&aid=2305594&group_id=36855&atid=418257 save implied links misfeature  Open  2008-11-17]
# 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: [https://sourceforge.net/tracker/?func=detail&aid=2770450&group_id=36855&atid=418260 2770450  Support for UTF-8 term names needed ASAP  Open  2009-04-17]
## New ticket for verification check: [https://sourceforge.net/tracker/?func=detail&aid=2815837&group_id=36855&atid=418260 2815837  Add Verification check for non ascii  Open  2009-07-02]


# Progress on wishlist for Buffalo:
#* 2116798  [https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260 Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd  Open  2008-09-17]
#* 2305594  [https://sourceforge.net/tracker/?func=detail&aid=2305594&group_id=36855&atid=418257 save implied links misfeature  Open  2008-11-17]




# Add verification check for non-ascii characters.
== Updated Tracker Items ==
#* This has become important because of changes to OE introduced by Jim Balhoff to allow UTF-8 text to be saved from OE2.
# [https://sourceforge.net/tracker/?func=detail&aid=2818549&group_id=36855&atid=418257 parent search ignores relationship type] <font color=blue> Fixed </font>
#* Fixes this ticket: [https://sourceforge.net/tracker/?func=detail&aid=2770450&group_id=36855&atid=418260 2770450  Support for UTF-8 term names needed ASAP  Open  2009-04-17]
# [https://sourceforge.net/tracker/?func=detail&aid=2815829&group_id=36855&atid=418260 Simplify 'save implied links'] <font color=blue> comment on tracker </font>
#* New ticket for verification check: [https://sourceforge.net/tracker/?func=detail&aid=2815837&group_id=36855&atid=418260 2815837  Add Verification check for non ascii  Open  2009-07-02]
## 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)
# [https://sourceforge.net/tracker/?func=detail&aid=2814791&group_id=36855&atid=418257 OBO merge doesn't work!] <font color=blue> Fixed </font>
# [https://sourceforge.net/tracker/?func=detail&aid=2801684&group_id=36855&atid=418257 OBO-Merge generates null-pointer exception] <font color=blue> Fixed </font>
# [https://sourceforge.net/tracker/?func=detail&aid=2818616&group_id=36855&atid=418257 stop panel changes if click on top] <font color=blue> comment on tracker </font>
# [https://sourceforge.net/tracker/?func=detail&aid=2812189&group_id=36855&atid=418257 GAZ.obo not displayed correctly in OBOEdit2.0] <font color=blue> Fixed </font>
## 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.
# [https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260 Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd] <font color=blue> DONE </font>
# [https://sourceforge.net/tracker/?func=detail&aid=2305594&group_id=36855&atid=418257 save implied links misfeature] <font color=blue> In progress </font>
## 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!)




==Discussion items==
==Discussion items==
* Bug Fixes:
* Version 2.1 finally ready for release after unexpected delays. Final touches and clean ups in progress.
** https://sourceforge.net/tracker/?func=detail&aid=2818549&group_id=36855&atid=418257
**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
* Switched to using OBO-Edit2 last week: Victoria Petri
** Several annotators use OE as a browser


* [http://sourceforge.net/tracker/?func=detail&aid=2821857&group_id=36855&atid=418257 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!


* More comments on OTE display with different reasoners, especially if there are disjoint violations (David)


==Action Items==
*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)




==Action Items==
*Harold will file bug report about Graphviz & paths (MAH joined call in middle of discussion of problem details)
*Amina: work on [https://sourceforge.net/tracker/?func=detail&aid=2821857&group_id=36855&atid=418257 problem with rule-based reasoner not running disjoint check]
*Amina: work on [https://sourceforge.net/tracker/?func=detail&aid=2705849&group_id=36855&atid=418257 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
==Links==
==Links==
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]

Latest revision as of 16:54, 30 June 2014

OBO-Edit Working Group, Thursday July 16th, 2009 8.30 a.m. PST

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


Agenda/Chair: Amina
Minutes: Midori
Attendees: Amina, Midori, Harold, Jen, Jane, David

Action items carried over

  1. Feature request: Simplify 'save implied links' interface so that it doesn't have different options and behaves as 'save for presentation' currently does.
    1. see below
    2. Amina - find out what does realize implied links do? If we don't need it delete
  2. Feature request: Optional Verification check to check if is_a child has same namespace as parent.
  3. AI: Jen has had problems showing all ancestors to root with graph editor- needs to investigate further to write bug report.
  4. Progress on wishlist for Buffalo:
    1. 2116798 Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd Open 2008-09-17
      1. see below
    2. 2305594 save implied links misfeature Open 2008-11-17
  5. Add verification check for non-ascii characters.
    1. This has become important because of changes to OE introduced by Jim Balhoff to allow UTF-8 text to be saved from OE2.
    2. Fixes this ticket: 2770450 Support for UTF-8 term names needed ASAP Open 2009-04-17
    3. New ticket for verification check: 2815837 Add Verification check for non ascii Open 2009-07-02


Updated Tracker Items

  1. parent search ignores relationship type Fixed
  2. Simplify 'save implied links' comment on tracker
    1. 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'
    2. 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 ...)
    3. might as well eventually remove 'all links' option (tho Amina will leave it in and add tooltips for now)
  3. OBO merge doesn't work! Fixed
  4. OBO-Merge generates null-pointer exception Fixed
  5. stop panel changes if click on top comment on tracker
  6. GAZ.obo not displayed correctly in OBOEdit2.0 Fixed
    1. affects any ontology with disjoint terms - they show as roots
    2. 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.
  7. Tool 2 save terms from 1 ontology rqd for reasoning in a 2nd DONE
  8. save implied links misfeature In progress
    1. 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!)


Discussion items

  • 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!
  • 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)


Action Items

Links

Back to OEWG Meeting agenda and minutes List