OEWG 20110503
OBO-Edit Working Group Meeting: Tuesday, May 5, 2011, 8:30am PDT
Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561
Agenda/Chair: Nomi Harris
Minutes:
Attendees:
Bug and Feature Trackers
Discussion items
- Chris Mungall will present the plan for the GO ontology editing environment.
Fixed since last meeting
- Cycle over mixed relationship types -> infinite loop
- Can't save fly_anatomy_XP.obo because OE goes into an infinite loop while running verification checks.
- Chris thought this was because fly_anatomy_XP has cycles over mixed relationship types, which is valid but was not considered valid when OBO-Edit was originally developed. This may be true, but in fact it turned out that the infinite loop was caused by a term that listed itself as an alternate ID. The validation process involves recursively checking the term's alternate ID, and since it's the same term, it just recurses over and over.
- Two ways to fix the infinite loop (it now does both):
- Before recursing on alt_id in the validation check, check whether it's the same as the primary ID.
- When reading in ontology, check for alt_id == primary_id and refuse to add it.
- adding words to dictionary removes uncommitted text edits
- Unfortunately, fixing this involved undoing a change I had made that fixed another, more minor bug:
Words added to dictionary in unedited term don't turn black immediately.
For now, we'll just have to live with the newly-added-to-dictionary word staying red until user does something that causes a commit (or moves to another term and then back).
- Unfortunately, fixing this involved undoing a change I had made that fixed another, more minor bug:
- ID Profile Mismatch dialogue box and multiple ontologies
- 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.
- Thanks to Midori for providing two tiny ontologies with ID profiles so I could test this.
- This message now lists the two ID profiles, so at least it's somewhat clearer. However, it still seems a bit random which one it chooses as the new one if you have multiple ontologies loaded, and I have not yet added the new feature to let you select which of multiple ID profiles you want to use. (If there are only two, it does let you choose between the two.)
- Bogus warning messages during validation: if you have a URL in a comment or definition, you get complaints about there not being spaces between "sentences" and lack of capital letters. Not sure what's the best way to address this. URL is not parsed as a single "word" but rather as multiple "sentences".
Currently working on
- Search for children misses some (unless reasoner on)
- If you turn on one of the reasoners, you find more children. Maybe the "child" and "parent" search aspects should be disabled if the reasoner is off?
- Is_a closure broken
- Filtered save with "is_a closure" checked doesn't save all the terms it should.
Next bugs to work on
- Filtered save with "child" aspect fails
- 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?
Discussion
- While testing 2.1-b12, one time it included Ancestor and Dependent in the Aspect menu even though the reasoner was off. After quitting and restarting, I couldn't get the problem to happen again. Let me know if anyone sees this happen.
- Should we disable "child" and "parent" search aspects if the reasoner is off? Fixing those searches might be hard.
- Still need to discuss with Chris
- Harold said that in GO, links are asserted, so you should be able to find all the children without needing the reasoner
- Midori said that, nonetheless, OE doesn't find all the children it should in GO.