OEWG 20110315

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OBO-Edit Working Group Meeting: Tuesday, March 15, 2011, 8:30am PDT (15:30 UK time rather than 16:30 like usual)

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

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Laurel Cooper, Marcus Chibucos, Midori Harris, Paola Roncaglia, Ramona Walls

Bug and Feature Tracker Updates

Discussion items

  • merge sometimes loses text details; sometimes can't undo merge
    • Sporadic and not new to 2.1b10
    • I have not been able to reproduce either problem. Midori and Ramona have both seen the loss of information on merge, but couldn't reproduce it reliably. Midori has found that sometimes she can't undo a merge, but it's unclear when/why that happens.
    • If anyone can give me a repeatable example of these problems, I will do my best to track them down.
  • Trying to help Paola to get her OBO-Edit behaving like Becky's. Problems with her dictionary. None of her problems appear to be OBO-Edit bugs.
  • have to click twice to view search results in text editor - This turned out to be another occurrence of a previously-observed issue where this happened to Harold when his oboedit_config/perspectives was out of date. Sure enough, when Ramona removed her perspectives subdirectory, it fixed this problem.
  • explanation component not working
    • Did it ever work? Can anyone remember when?
  • Michael Ashburner reported, "Every now and again a Tree Editor window gets the shakes, the terms spontaneously travelling up & down the window. This cannot be cured - except by killing the window."
    • This may be the same problem reported by Harold a few years ago: https://sourceforge.net/tracker/index.php?func=detail&aid=2024992&group_id=36855&atid=418257 "When I select a term from a search, the tree editor moves to the term, but then continues to scroll up without stopping when I then touch another area such as the text editor. In fact, if I select a term from the search, the tree editor jumps to the term with it being on the top of the window. If I then so much has hover my mouse over the search screen again, the tree editor starts scrolling up again, no touch or click needed."
      • Harold reported that this never happened to him again. Has anyone else observed it?

Fixed since last meeting

  • Words added to dictionary in unedited term don't turn black immediately
    • If you are editing a term and OBO-Edit colors a word red because it thinks it's misspelled, you can add the word to the dictionary and then it turns black. However, if you loaded an ontology and there were words that OBO-Edit didn't recognize, adding them to the dictionary didn't make them turn black right away. Now fixed.
  • Repeated word warnings: warned about some repeated digits (e.g., "7.7-dimethyl-whatever"). Now all of the digits are in the allowed-repeats list.
  • Search term Filter returning wrong results
    Some filters give wrong answers unless reasoner turned on
    • Fixed: search aspects (Ancestor and Descendent) that require the reasoner don't appear in the Aspect list unless the reasoner is on.
      • Added tooltip to "in" label before aspect that says "Note: Ancestor and Descendent are available only if the reasoner is on."
        Added notes to user guide about ancestor/descendent only being available if reasoner is on.

Currently working on

Next bugs to work on

  • 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.
  • scroll lock (aka lock view) for global OTE - If I click on terms in the locked OTE, it doesn't show them in the Text Editor or other components, and it should, right?
  • There are a bunch of other priority-7 feature requests -- are they all still priority 7? Which should I look at first?
  • There are a bunch of priority-6 bugs in the bug tracker--any I should look at first?


  • Explanation component: Midori found that it (at least sometimes) works on SO, and sent Nomi an example.
  • OTE window getting the "shakes" (Michael Ashburner reported)--no one else (who was on the call) has seen this.
  • Marcus is trying to create complex cross-product ontologies from multiple ontologies. Cell is one of the ontologies. When he tries to save it, he gets a critical error because there's a comment that has an extended character. Is there a way to add a new feature to "Ignore critical errors in other ontologies"?
    • Maybe we could have a "CRITICAL ERROR--save anyway?" option (like it already does if there are just warnings).
    • Some ontologies have so many warnings, it says "stopped counting", and you can't see all the errors. Would be good to have a way to see all of them. (Bump up error cutoff?)
    • Would be nice if errors were grouped by type--e.g., all spelling errors together, all repeated word complaints, etc. Would be even nicer if you could choose which types of errors to show.
      • Fully implementing that would be non-trivial, but perhaps it would be straightforward to sort the errors somehow so that similar sorts of errors appeared together in the list.
  • Loading multiple ontologies--PATO, GO, cell etc, Marcus gets message "ID profile mismatch--use profile loaded from the file"? Which ontology file is it referring to? It should say which. (Marcus will post this as a bug.)
  • Marcus is creating terms in his ontology (but has also loaded other ontologies). Create a term, name term, commit it. Then he tries to create the cross product. Some of these terms from different ontologies have the same or similar names. Say I name a term in my ontology "interaction with host", which is also a GO term, and then the genus autocompletes, but you end up seeing two lines that say "interaction with host" and you can't tell which one to click on. If it showed ID or namespace in that autocomplete menu, that would be helpful.
    • Nomi said that she understands how that would be annoying, but due to the way the autocomplete menu works, that may not be possible.
    • Ramona suggests using ontology-specific versions of term names. For example, if the GO term is "anatomical structure", in plant ontology they call it "plant anatomical structure".
      • Marcus: that limits the ability to import the terms into other ontologies (but it's still a good idea in some cases).
  • Paola: if she wants to add a dbxref or a synonym, the window sort of blanks out showing only a tiny fraction on the top of the window. She has to double-click to put things in. She's seen this for both the dbxref and synonym windows.
    • Ramona: when you used to try to add a dbxref, in the past the text would disappear and you couldn't see what you were typing, but she thinks that was fixed. The dbxref/synonym editing windows are tiny (esp. on a laptop) so it can be hard to see what's in them.
    • Midori said she still sometimes gets the disappearing text in the dbxref/synonym windows.
    • Ramona: when this happens, it's because your mouse has gone into the wrong place. Be sure to double-click in the right place. If it goes away when you double-click, click it again and start over again.
      • Ramona hasn't seen this problem recently--she thinks it's been fixed.
      • Midori said when she sees it, it's when she's adding a dbxref for a synonym rather than for a definition.
    • Nomi sees problematic behavior in the dbxref/synonym panels when the Text Editor window is its usual size, but if you make it bigger, it works better. Try undocking your Text Editor window if you're doing a lot of text editing.
  • Ramona would like to be able to move undocked windows behind other windows instead of being in front of everything. (The user guide window can do this.)
    • Unfortunately, this will not be easy to fix, because the undocked window stuff is handled by a third-party package (infonode.docking) and it appears that undocked--aka floating--windows are DEFINED as floating in front of the other components. The user guide window is different because it is created as a new window by a different method (and it can't be docked--it's not a dockable component).
  • Marcus: when you use the magnifying glass in the user guide, you get duplicate items, and one of the duplicates is empty and the other has the info.
    • Nomi remembers having fixed this before (others agreed). She will look into it.
  • Someone asked whether there's a way to see the most recently modified items in the SourceForge bug tracker. There isn't a way to sort by Last Modified, but this query will show you tracker items (bug or feature) that were modified in 2011 and that are still open.


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