OBO-Edit Working Group Meeting: Tuesday, March 1, 2011, 8:30am PST
Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
Agenda/Chair: Nomi Harris
Minutes: Rebecca Foulger
Attendees: Nomi Harris, Ramona Walls, Rebecca Foulger
Bug and Feature Tracker Updates
- 2.1-b10 released on 2/23/2011 (see the 2.1beta10 page for details)
- (2.1-b9 was an internal release, tested by a few people on 2/18/2011)
Fixed since last meeting
- built in icons missing
- Added generic icons (single letters, numbers, Greek letters, etc.) to the set of built-in icons. (The icons were originally generated by the script src/org/oboedit/gui/resources/icons/svg_script.pl).
- Made window for showing built-in icons bigger (was a single long strip).
- search result highlight color too dark
- The selected search result was highlighted in a too-dark blue that made it almost impossible to read the text. Now it uses the same highlight color as the Ontology Tree Editor (currently, medium-light blue).
- Also fixed selection color in dropdown autocomplete list--was the same too-dark blue as search results; now it's the same as in the OTE.
- java.lang.object@... appears in autocomplete results
- https://sourceforge.net/tracker/?func=detail&aid=2890891&group_id=36855&atid=418257 Obsolete terms appear in autocomplete dropdown lists].
- Added user-configurable ability to filter obsolete terms from search results and autocomplete dropdown lists. Can be set via a checkbox in Configuration Manager -> Behavior (but changing it requires restart).
- Fixed some omissions in saved header fields
- data-version header field was not getting round-tripped--now it is.
- saved-by should appear in saved OBO file
- Updates to user guide:
- Added user guide page on "Color-coding Multiple Ontologies by Namespace".
- Merged redundant "Reasoner Manager" page into "The Reasoner and the Interface"
- Added warning about the reasoner and memory; removed descriptions of obsolete reasoners
Issues and action items carried over from last meeting:
Currently working on:
- 2.1beta10 merge loses text details
- Midori says the problem showed up some time between 2.1b7 and 2.1b10
- When she merged terms A and B, synonyms from A disappeared, and A's name didn't become a synonym for B. The definitions also weren't merged.
- Ramona said, "Last week when I was trying to merge a term, it [she means 2.1b9] didn't work properly (wouldn't show source ID as alternate ID). I tried it three or four times, then it finally worked. I may have restarted the program in between it working and it not working"
- I tried merging several terms in 2.1b10 and it all worked as it should. It sounds like there's some scenario in which it doesn't work. (It doesn't seem to me that it's a bug that's new to 2.1b10--it could have been around for a while). If anyone can give me a repeatable example of this problem, I will track it down.
- Search term Filter returning wrong results
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 Some filters give wrong answers unless reasoner turned on
Next bugs to work on:
- Is_a closure broken
- 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.
- explanation component not working
- Users are testing 2.1b10
- Nomi would like more testing on the option to turn the 'filter for returning obsolete terms' on and off (under configuration manager: note that it requires a restart of OBO-Edit to remember the settings) because it required a lot of changes in different places of the code.
- Ramona noted that in the plant ontology, the obsolete search filtering seemed to work for some searches and not others, but on further investigation, it turned out that the search filtering was working correctly. The obsolete term was coming up as a synonym for a non-obsolete term, so it showed up in the completion list if you searched for "Any text field" or "Name or synonym", but not if you just searched for "Name".
- We discussed the term-merging problem that Midori reported. Ramona had this happen in 2.1b9. This seems to be a sporadic problem. It is almost certainly not new to 2.1b10 (since Ramona saw it in 2.1b9). Need to figure out how to trigger this problem before it can be fixed.
- Ramona would like a warning if there's a non-standard symbol in the DBxref description field (not the ID field). Low priority item, and already submitted as a feature request. (If there are non-standard symbols in that field, then some other software used by some of her collaborators chokes on it.)
- The reasoner is still too slow to leave on while editing. Nomi would like more feedback on any reasoner bugs.
- More testing of "exclude obsolete terms from search filter"
- Users to note and report when information (e.g. secondary ID) gets lost when merging terms
- Nomi is working on the bugs listed above