OEWG 20110208
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:
Attendees:
Action items carried over
Bug and Feature Tracker Updates
Discussion items
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
=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.
Currently working on
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 or otherwise indicated."
- Longer term possibilities--see discussion in 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 or otherwise indicated."
Next bugs to work on:
- 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 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.
- 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.
- 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.
- This works for me--can someone else test it and confirm that it's fixed?
- 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.
- 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 quetting/etc.
- 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.
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
none
Action Items
- Nomi will email wg mailing list to remind members how to unsubscribe if they want.
- Terry will write instructions on how to use renderers to color terms by namespaces. Nomi will add to the user guide.
- Ramona will submit bug report on disappearing relation icons.
- Nomi will add note about reasoner & memory to user guide.
- Nomi will look at autocomplete selection bug again.