OEWG 20110208: Difference between revisions

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[[Category:OBO-Edit working group]]
OBO-Edit Working Group Meeting: Tuesday, February 8th, 2011, 8:30am PST
OBO-Edit Working Group Meeting: Tuesday, February 8th, 2011, 8:30am PST


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Agenda/Chair: Nomi Harris<br />
Agenda/Chair: Nomi Harris<br />
Minutes: <br />
Minutes: Rebecca Foulger<br />
Attendees: <br />
Attendees: Nomi, Harold, Terry, Karen, Midori, Rebecca<br />
 
==Action items carried over==
 


== Bug and Feature Tracker Updates ==
== Bug and Feature Tracker Updates ==
Line 19: Line 17:


==Discussion items==
==Discussion items==
* GO ref genome and annotation calls are moving to Tuesdays at 8am PST, conflicting with the OE calls.  Should we pick a different day of the week, or just start at 9 instead of 8:30?
** The annotation and reference genome calls are now on Tuesdays 4-5pm GMT (8am Californian time), which means they will often clash with the OBO-Edit working group calls.
** The AmiGO hub meetings are on the 1st and 3rd Tuesday of the month (normally 8:30-9:30 Californian time, 16:30-17:30 UK), which will also clash.
** There may be another free phoneline we can use- people will investigate. Clackpoint tried out by Jen Deegan in the past wasn't successful, and it's thought that skype calls will so many users will not be clear.
** AI: Karen will check with Rama about whether the AmiGO hub meetings are still active, then we can make a decision about whether to move days or times for the OEWG calls.
** When the times are set, Rebecca will add them to the GO calendar, so no-one else will book the GO line at the same time. The next meeting may or may not be on Tuesday March 1st at 8:00 California time.
* UPDATE: AmiGO hub meetings are no longer happening.  '''We will hold OEWG meetings on the 1st and 3rd Tuesday of the month at 8:30am California time (16:30 UK time).  The next meeting will be Tuesday, March 1st, at 8:30 California time.'''


===Fixed since last meeting:===
===Fixed since last meeting:===
* Users with older Macs that don't have Java 1.6 couldn't launch OE: http://sourceforge.net/tracker/?func=detail&aid=3150956&group_id=36855&atid=418257
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3165309&group_id=36855&atid=418257 hitting return just selects first term from dropdown list]<br />[https://sourceforge.net/tracker/index.php?func=detail&aid=1897960&group_id=36855&atid=418257 irritating selection bug in autocompletion-searches (b30)]
<br />
** Several similar bug reports were closed as fixed in 2.1-b7, but they weren't--it would still choose the first item in the list if you moused down in the list and then hit return.  Now it's really fixed (yay!).
===Carried over from last meeting:==
* Users with older Macs that don't have Java 1.6 (such as Ramona) couldn't launch OE--see also [http://sourceforge.net/tracker/?func=detail&aid=3150956&group_id=36855&atid=418257 The JVM could not be started]
** Fixed--OE installer will now work even if you only have Java 1.5.  (Ramona has tested--it worked for her.)
** Pre-release available for those who need it--ask Nomi in email.
 
===Issues and action items carried over from last meeting:===
* Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
* Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
** Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.
** Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.
<br />
* Terry wrote instructors for configuring a renderer to color terms by namespace (Thanks, Terry!). Nomi needs to add this to user guide.
==Currently working on==
* Nomi will also add comments on reasoner + memory to user guide.
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3169726&group_id=36855&atid=418257 Search term Filter returning wrong results]
** Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
[https://sourceforge.net/tracker/index.php?func=detail&aid=1899612&group_id=36855&atid=418257 Some filters give wrong answers unless reasoner turned on]
** Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quitting/etc.
** Discussed with Chris. Agreed on short-term fix: "if an aspect of a search cannot be performed without the reasoner, then it should be greyed out or otherwise indicated."
*** Longer term possibilities--see discussion in [https://sourceforge.net/tracker/index.php?func=detail&aid=1899612&group_id=36855&atid=418257 Some filters give wrong answers unless reasoner turned on]
 
 
 
 
===Next bugs to work on:===
* [https://sourceforge.net/tracker/?func=detail&aid=2890891&group_id=36855&atid=418257 Obsolete terms appear in autocomplete dropdown lists]. Questions:
** Should I make ALL autofill suggestions exclude obsolete terms? That should be doable. Otherwise, it's going to be tricky, because the autofill code doesn't know what the term is going to be used for.
*** Yes; everyone likes this idea.
** This bug report also mentions a feature request that's come up before: please show the namespace each term belongs to. This feature may be more important than it used to be because more people are working with multiple ontologies (which may contain duplicate terms).
*** Is this a high-priority feature?
*** As indicated in [https://sourceforge.net/tracker/index.php?func=detail&aid=1761449&group_id=36855&atid=418260 a reply to this feature request], the terms can be colored by namespace by constructing a term renderer in the Global Filters interface. Would someone like to volunteer to write up instructions on how to do that, and I'll add it to the user guide?  (We could even make that behavior the default, if people like the idea.)
*** Agree that new feature isn't a high priority. Terry will write up instructions on setting up renderers.
 
* [https://sourceforge.net/tracker/?func=detail&aid=2823197&group_id=36855&atid=418257 Some disjoint_from relationships impossible to delete]
** This works for me--can someone else test it and confirm that it's fixed?
*** Nobody else has done the kind of work that would run into this problem.
* ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago).  How important is this?
* ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago).  How important is this?
** Most wg members don't even know what it does! Nomi will bring it up with Chris.
** Most wg members don't even know what it does! Nomi will bring it up with Chris.


** Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
===Currently working on:===
** Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quetting/etc.
* [https://sourceforge.net/tracker/?func=detail&aid=2890891&group_id=36855&atid=418257 Obsolete terms appear in autocomplete dropdown lists].
** Current status: implemented removal of obsolete terms from autocomplete lists for searches of "Any text field" (will implement for other types of searches.
*** This extra test slows down creation of autocomplete list.
*** Accordingly, Becky suggested making this a user-configurable option (whether or not to exclude obsolete terms from autocomplete lists).  Will add to Configuration Manager.
**** Default will be NOT to exclude obsolete terms from autocomplete lists (i.e., the current behavior)--user will have to change this option in Configuration Manager to make it exclude obsolete terms.
*** I'm also looking into ways to speed up autocomplete.
*** There was a request to show obsolete terms as red in the autocomplete list. Nomi isn't sure how complicated it would be but suggests Terry adds it as a feature request.
* [https://sourceforge.net/tracker/?func=detail&aid=3170843&group_id=36855&atid=418257 built in icons missing] (Ramona)
** Terry has sent a set of ready-made icons to Nomi (thank you).
** Nomi: Should we add those to the set of icons that come with OE, because "Browse built-in icons" is already slow, and might be slower if we add a lot more icons.
*** UPDATE: it's not much slower, so I'll go ahead and include them.
** On a related note, Nomi looked into the issue where when you add a new relationship that doesn't have a relationship icon, it is rendered in the Graph Editor in an unreadable font.  She tried to add tooltips to show the relationship name when you hover over the relationship icon, but it turns out that the classes used in the Graph Editor don't provide that functionality.  Oh well.


===Next bugs to work on:===
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3169726&group_id=36855&atid=418257 Search term Filter returning wrong results]<br />[https://sourceforge.net/tracker/index.php?func=detail&aid=1899612&group_id=36855&atid=418257 Some filters give wrong answers unless reasoner turned on]
** Discussed with Chris. Agreed on short-term fix: "if an aspect of a search cannot be performed without the reasoner, then it should be greyed out [i.e., disabled] or otherwise indicated."
** Longer term possibilities--see discussion in [https://sourceforge.net/tracker/index.php?func=detail&aid=1899612&group_id=36855&atid=418257 Some filters give wrong answers unless reasoner turned on]
* [https://sourceforge.net/tracker/?func=detail&aid=2309391&group_id=36855&atid=418257 Bad handling of unrecognized relation (text editor et al.)]
* [https://sourceforge.net/tracker/?func=detail&aid=2309391&group_id=36855&atid=418257 Bad handling of unrecognized relation (text editor et al.)]
** I looked into this some--will not be simple to fix.  Has to do with how dangling objects (e.g., unrecognized relations) are handled in different components.
** I looked into this some--will not be simple to fix.  Has to do with how dangling objects (e.g., unrecognized relations) are handled in different components.
* Terry says when you run the reasoner it gives you a line indicating an error/warning, but not an answer about why the relationship is wrong. Nomi suggested he submit a bug report on high priority.
* Terry and Jen have both submitted bug reports about the explanation manager. Nomi will get to it once she's finished the fixes she's working on.


===Issues raised in meeting===
* Ramona's problem launching 2.1beta8 traced to java version: she has 1.5, but OE needs 1.6. Nomi will help Ramona install Java 1.6.
* Ramona has custom relations, and their icons have disappeared. She'll put in a bug report.
* Becky put in bug report on autocomplete selection. Sounds familiar to several of us. Nomi will look at it.
== Demo ==
== Demo ==
none
none


==Action Items==
==Action Items==
* Nomi will email wg mailing list to remind members how to unsubscribe if they want.
* Rescheduling OEWG meeting [DONE]
* Terry will write instructions on how to use renderers to color terms by namespaces. Nomi will add to the user guide.
** Karen will check whether AmiGO Hub meeting is still happening on 1st and 3rd Tuesdays [DONE]
* Ramona will submit bug report on disappearing relation icons.
** Rebecca will add OEWG meeting dates to GO calendar [DONE]
* Nomi will add note about reasoner & memory to user guide.
* Nomi to add Terry's instructions on how to use renderers to color terms by namespaces to the user guide. [DONE]
* Nomi will look at autocomplete selection bug again.
* Nomi will add note about reasoner & memory to user guide. [DONE]
* Nomi will make exclusion of obsolete terms from autocomplete lists user-configurable. [DONE]
* Harold asked for more prominent announcements for new OE releases. Midori said you could ask SourceForge to let you know of new releases (but SF is a bit buggy) but Nomi will make the announcements clearer. [DONE, I think]
* Nomi will add generic relationship icons (letters of the alphabet, etc.) to OE's set of built-in icons [DONE]


==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 17:46, 30 June 2014

OBO-Edit Working Group Meeting: Tuesday, February 8th, 2011, 8:30am PST

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

Agenda/Chair: Nomi Harris
Minutes: Rebecca Foulger
Attendees: Nomi, Harold, Terry, Karen, Midori, Rebecca

Bug and Feature Tracker Updates

Discussion items

  • GO ref genome and annotation calls are moving to Tuesdays at 8am PST, conflicting with the OE calls. Should we pick a different day of the week, or just start at 9 instead of 8:30?
    • The annotation and reference genome calls are now on Tuesdays 4-5pm GMT (8am Californian time), which means they will often clash with the OBO-Edit working group calls.
    • The AmiGO hub meetings are on the 1st and 3rd Tuesday of the month (normally 8:30-9:30 Californian time, 16:30-17:30 UK), which will also clash.
    • There may be another free phoneline we can use- people will investigate. Clackpoint tried out by Jen Deegan in the past wasn't successful, and it's thought that skype calls will so many users will not be clear.
    • AI: Karen will check with Rama about whether the AmiGO hub meetings are still active, then we can make a decision about whether to move days or times for the OEWG calls.
    • When the times are set, Rebecca will add them to the GO calendar, so no-one else will book the GO line at the same time. The next meeting may or may not be on Tuesday March 1st at 8:00 California time.
  • UPDATE: AmiGO hub meetings are no longer happening. We will hold OEWG meetings on the 1st and 3rd Tuesday of the month at 8:30am California time (16:30 UK time). The next meeting will be Tuesday, March 1st, at 8:30 California time.

Fixed since last meeting:

Issues and action items carried over from last meeting:

  • Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
    • Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.
  • Terry wrote instructors for configuring a renderer to color terms by namespace (Thanks, Terry!). Nomi needs to add this to user guide.
  • Nomi will also add comments on reasoner + memory to user guide.
    • Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
    • Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quitting/etc.
  • ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago). How important is this?
    • Most wg members don't even know what it does! Nomi will bring it up with Chris.

Currently working on:

  • Obsolete terms appear in autocomplete dropdown lists.
    • Current status: implemented removal of obsolete terms from autocomplete lists for searches of "Any text field" (will implement for other types of searches.
      • This extra test slows down creation of autocomplete list.
      • Accordingly, Becky suggested making this a user-configurable option (whether or not to exclude obsolete terms from autocomplete lists). Will add to Configuration Manager.
        • Default will be NOT to exclude obsolete terms from autocomplete lists (i.e., the current behavior)--user will have to change this option in Configuration Manager to make it exclude obsolete terms.
      • I'm also looking into ways to speed up autocomplete.
      • There was a request to show obsolete terms as red in the autocomplete list. Nomi isn't sure how complicated it would be but suggests Terry adds it as a feature request.
  • built in icons missing (Ramona)
    • Terry has sent a set of ready-made icons to Nomi (thank you).
    • Nomi: Should we add those to the set of icons that come with OE, because "Browse built-in icons" is already slow, and might be slower if we add a lot more icons.
      • UPDATE: it's not much slower, so I'll go ahead and include them.
    • On a related note, Nomi looked into the issue where when you add a new relationship that doesn't have a relationship icon, it is rendered in the Graph Editor in an unreadable font. She tried to add tooltips to show the relationship name when you hover over the relationship icon, but it turns out that the classes used in the Graph Editor don't provide that functionality. Oh well.

Next bugs to work on:

Demo

none

Action Items

  • Rescheduling OEWG meeting [DONE]
    • Karen will check whether AmiGO Hub meeting is still happening on 1st and 3rd Tuesdays [DONE]
    • Rebecca will add OEWG meeting dates to GO calendar [DONE]
  • Nomi to add Terry's instructions on how to use renderers to color terms by namespaces to the user guide. [DONE]
  • Nomi will add note about reasoner & memory to user guide. [DONE]
  • Nomi will make exclusion of obsolete terms from autocomplete lists user-configurable. [DONE]
  • Harold asked for more prominent announcements for new OE releases. Midori said you could ask SourceForge to let you know of new releases (but SF is a bit buggy) but Nomi will make the announcements clearer. [DONE, I think]
  • Nomi will add generic relationship icons (letters of the alphabet, etc.) to OE's set of built-in icons [DONE]

Links

Back to OEWG Meeting agenda and minutes List