OEWG 20110517: Difference between revisions

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[[Category:OBO-Edit working group]]
OBO-Edit Working Group Meeting: Tuesday, May 17, 2011, 8:30am PDT
OBO-Edit Working Group Meeting: Tuesday, May 17, 2011, 8:30am PDT


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Agenda/Chair: Nomi Harris<br />
Agenda/Chair: Nomi Harris<br />
Minutes: <br />
Minutes: Nomi <br />
Attendees: <br />
Attendees: Nomi, Chris Mungall, Heiko Dietze, Karen Christie, Midori Harris, Ramona Walls, Rebecca Foulger<br />


== Bug and Feature Trackers ==
== Bug and Feature Trackers ==
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==Discussion items==
==Discussion items==
* OBO-Edit 2.1-beta13 released on May 16--[http://wiki.geneontology.org/index.php/OBO-Editv2.1beta13 release notes are here]


===Fixed since last meeting===
===Fixed since last meeting===
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** Fixed in 2.1-b13
** Fixed in 2.1-b13


* As suggested by OEWG, all search aspects are once again available in search aspect menu.  If user selects an aspect (Ancestor or Descendant) that requires reasoning and the reasoner isn't on, they get a pop-up error message: "If you want to search Ancestors or Descendants, you must first turn on the Reasoner (use the Reasoner Manager component to do that).[[File:aspect-message.jpg]]
* As suggested by OEWG, all search aspects are once again available in search aspect menu.  If user selects an aspect (Ancestor or Descendant) that requires reasoning and the reasoner isn't on, they get a pop-up error message:  
** (The previous solution--leaving Ancestor and Descendant out of the aspect menu
[[File:aspect-message.png]]
when reasoner was off--confused users.)
** (The previous solution--leaving Ancestor and Descendant out of the aspect menu when reasoner was off--confused users.)
* Also, you can (once again) do filtered saves with Ancestor and Descendant even when the reasoner is off, because the filtered save method can start a reasoner.
* Also, you can (once again) do filtered saves with Ancestor and Descendant even when the reasoner is off, because the filtered save method can start a reasoner.
** Some users complained that these filtered saves that silently invoked the reasoner took so long they thought OE had crashed. Now the Progress window says "This filtered save requires the reasoner--please be patient."  (Note that the progress string is limited in length--if you make it longer than that it gets cut off.)
** Some users complained that these filtered saves that silently invoked the reasoner took so long they thought OE had crashed. Now the Progress window says "This filtered save requires the reasoner--please be patient."  (Note that the progress string is limited in length--if you make it longer than that it gets cut off.)
* [http://sourceforge.net/tracker/?func=detail&aid=3302649&group_id=36855&atid=418257 Add verification check for single intersection_of tag]
* Changed wording of messages in OE and in installer about the fact that memory allocation is limited to 1860M unless you have a 64-bit JVM.
** No way to change installer to conditionally allow >1860M if JVM is 64-bit, but at least wording now explains why there's a limit and how you can get around it.
[[File:memory-message.png]]


===Next bugs to work on===
===Next bugs to work on===
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* [http://sourceforge.net/tracker/?func=detail&aid=2309391&group_id=36855&atid=418257 Bad handling of unrecognized relation (text editor et al.)]
* [http://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.
* [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id= Bugs with priority 6] -- Let's talk about which of these I should look at next.
* [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id= Bugs with priority 6], [http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418260&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter&mass_category=&mass_priority=&mass_resolution=&mass_assignee=&mass_artgroup=&mass_status=&mass_cannedresponse=&_visit_cookie=ed025b4c35c82a5c1582b774b7676154 Features with priority 6-7]
** Let's talk about which of these I should look at next.


===Discussion===
===Discussion===
* A user was puzzled that older versions of OBO-Edit included Ancestor and Descendent in the Aspect menu but the latest OE didn't. We explained that OE can't get the right answers to Ancestor and Descendent searches unless the reasoner is on, so these searches are not included in the Aspect menu when the reasoner is off.
* Action Item:  OEWG members will look at the bug and feature trackers (sorted in descending order by priority) and reprioritize where appropriate (or ask Nomi to reprioritize if they don't have permission to change priorities) and suggest to Nomi which bugs to look at next.
** Nomi described the attempts she had made to make this more obvious (none of which succeeded in making it particularly obvious), and then suggested a new possible approach: leave Ancestor and Descendent in Aspect menu, but if user chooses one when Reasoner is off and tries to do a search, they get a popup error message explaining that they need to turn the reasoner on to do that search.
* Karen reported that she can remove discriminating relationships from cross-products, but there's no trashcan icon for removing the intersection genus. Sometimes she wants to get rid of the whole cross product. She has tried clearing out all the fields and committing, but that doesn't (always?) work.
*** Attendees liked that solution.
** Midori suggested a workaround--do it in the parent editor
** Chris said that it should be possible to make OBO-Edit run a simple reasoner (such as the OnTheFly reasoner) to do ancestor searches (as long as they are over all ancestors, not limited by a specific relationship type)  without turning on the full reasoner.
** Ramona said that sometimes she can't get rid of these relationships when she's been running the reasoner; if she turns off the reasoner and restarts, it works.  Karen said she didn't have the reasoner on.
*** Nomi said that could be added as a feature request but it probably would not be quick to implement.
** The problem where you can't delete some relationships appears to be intermittent.
* Filtered save silently invokes a reasoner if the user asks to save inferred links
** Chris M said you can have more than one discriminating relationship and you might want to delete those individually, but you'd never want to delete the genus and leave the differentia behind. So we should keep the trashcan for the discriminating relationship, but also add a new overall trashcan for getting rid of the whole thing.
** This can be slow--it was suggested that OE should pop up some sort of warning so that the user doesn't think OE has frozen up.
*** Karen will add a tracker item for this.
** Nomi thought maybe running the reasoner for is_a closure filtered save would help fix it.
* Karen: if you obsolete a term, you can no longer edit its definition, but documentation says you canFor GO, editors need to add OBSOLETE to beginning of definition. If you don't remember to do that before you obsolete the term, you can't edit the definition and you can't unobsolete the term.  (Can still edit comment field but not definition.)  
*** Chris didn't think that would help. (?? Did I remember that correctly??)
** OBO-Edit could automatically add OBSOLETE: to beginning of def--but what if other projects don't want that?
**** I don't remember whether Chris said anything. I found when I was testing that it didn't make any difference if I ran the reasoner before saving or not; the is_a closure didn't work as expected (except sort of in beta4). I don't know whether the reasoner was running during the save, nor do I have any idea whether it would help if it did. -Midori
*** Could that be a config option?  Nomi: yes, but it's kind of a pain to add that.
* Search for children misses some (unless reasoner on)
** Nomi: how about you can still edit definition after obsoleting a term, but it pops up a warning ("Term is obsolete--are you sure you want to edit definition?")
** Nomi needs a small test case this. Someone (Marcus??) said they'd make one.
*** People liked that idea
 
** Ramona suggested:  the warning you get when you're about to obsolete a term could mention that you can't edit the definition after obsoleting
  Marcus is making cross products with PATO as intersection genus, GO as differentia (?), saving with complete is_a closure [I didn't get this all down, can someone help fill it in?]
*** Nomi liked that idea a lot because it would be very easy (just add text to a message).
** In cross-product intersection box, it shows ugly java.lang.Object@303e7b (the gibberish after '@' seems to be unique per OE launch) (minor edit -Midori)
** At any rate, documentation should match behavior (either definition is editable in obsolete terms or it's not).
** Midori sees that too IF she doesn't load the other ontologies (with allow dangling refs)If she loads the other ontologies, they look ok. (minor edit -Midori)
* Action item: GO meeting attendees, please take note of any OBO-Edit problem reports or requests and send them to Nomi.
*** Yes - Marcus and I are both making cross-products using terms from PATO, GO, ChEBI, etc. The terms with the cross-product definitions live in our phenotype ontologies (FYPO for me), and we can load just the phenotype ontology, all of the ontologies used in xp defs, or a subset of the total. Terms from ontologies I load look fine in the cross-product panel; anything from an ontology I don't load gets a java.lang.Object@wackiness. If I load GO and FYPO, for example, FYPO terms and GO terms look good, but PATO and ChEBI terms show up as java.lang.Objects. (added -Midori)
** If you're making a cross-product ontology, you can't reasonably ask users to load all the other ontologies
** Chris said the java.lang thing should be posted as a bug report
** Feature request: way to save just the terms from the ontologies that are needed in the cross-product ontologies (save is_a closure is intended to do this but doesn't really work right)


==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 17:56, 30 June 2014

OBO-Edit Working Group Meeting: Tuesday, May 17, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Chris Mungall, Heiko Dietze, Karen Christie, Midori Harris, Ramona Walls, Rebecca Foulger

Bug and Feature Trackers

Discussion items

Fixed since last meeting

Can't restrict ancestor search by relation type in 2.1b12 (same bug)

    • If you have the reasoner on and select "ancestor" or "descendant" as the search aspect, it's supposed to add a list of relations and the label "can be reached via", but that stopped happening in 2.1-b11 or 12
    • Fixed in 2.1-b13
  • Search for children is missing some (unless reasoner on)
    • This was an old bug. Turned out that when links to children were being collected, the code erroneously took the PARENT of each link instead of the child. (But when the reasoner was on, there was a different loop, which is why the child search worked ok with the reasoner on.)
    • Fixed in 2.1-b13
  • Filtered save with "child" aspect throws exception
    • Fixed in 2.1-b13
  • As suggested by OEWG, all search aspects are once again available in search aspect menu. If user selects an aspect (Ancestor or Descendant) that requires reasoning and the reasoner isn't on, they get a pop-up error message:

    • (The previous solution--leaving Ancestor and Descendant out of the aspect menu when reasoner was off--confused users.)
  • Also, you can (once again) do filtered saves with Ancestor and Descendant even when the reasoner is off, because the filtered save method can start a reasoner.
    • Some users complained that these filtered saves that silently invoked the reasoner took so long they thought OE had crashed. Now the Progress window says "This filtered save requires the reasoner--please be patient." (Note that the progress string is limited in length--if you make it longer than that it gets cut off.)
  • Add verification check for single intersection_of tag
  • Changed wording of messages in OE and in installer about the fact that memory allocation is limited to 1860M unless you have a 64-bit JVM.
    • No way to change installer to conditionally allow >1860M if JVM is 64-bit, but at least wording now explains why there's a limit and how you can get around it.

Next bugs to work on

Discussion

  • Action Item: OEWG members will look at the bug and feature trackers (sorted in descending order by priority) and reprioritize where appropriate (or ask Nomi to reprioritize if they don't have permission to change priorities) and suggest to Nomi which bugs to look at next.
  • Karen reported that she can remove discriminating relationships from cross-products, but there's no trashcan icon for removing the intersection genus. Sometimes she wants to get rid of the whole cross product. She has tried clearing out all the fields and committing, but that doesn't (always?) work.
    • Midori suggested a workaround--do it in the parent editor
    • Ramona said that sometimes she can't get rid of these relationships when she's been running the reasoner; if she turns off the reasoner and restarts, it works. Karen said she didn't have the reasoner on.
    • The problem where you can't delete some relationships appears to be intermittent.
    • Chris M said you can have more than one discriminating relationship and you might want to delete those individually, but you'd never want to delete the genus and leave the differentia behind. So we should keep the trashcan for the discriminating relationship, but also add a new overall trashcan for getting rid of the whole thing.
      • Karen will add a tracker item for this.
  • Karen: if you obsolete a term, you can no longer edit its definition, but documentation says you can. For GO, editors need to add OBSOLETE to beginning of definition. If you don't remember to do that before you obsolete the term, you can't edit the definition and you can't unobsolete the term. (Can still edit comment field but not definition.)
    • OBO-Edit could automatically add OBSOLETE: to beginning of def--but what if other projects don't want that?
      • Could that be a config option? Nomi: yes, but it's kind of a pain to add that.
    • Nomi: how about you can still edit definition after obsoleting a term, but it pops up a warning ("Term is obsolete--are you sure you want to edit definition?")
      • People liked that idea
    • Ramona suggested: the warning you get when you're about to obsolete a term could mention that you can't edit the definition after obsoleting
      • Nomi liked that idea a lot because it would be very easy (just add text to a message).
    • At any rate, documentation should match behavior (either definition is editable in obsolete terms or it's not).
  • Action item: GO meeting attendees, please take note of any OBO-Edit problem reports or requests and send them to Nomi.

Links

Back to OEWG meeting agenda and minutes list