OBO-Edit Working Group Meeting: Thursday, July 21, 2011, 8:30am PDT
Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
Agenda/Chair: Nomi Harris
Minutes: Rebecca Foulger
Nomi Harris (LIVE at the EBI!),
Bug and Feature Trackers
- OBO-Edit 2.1-b16 released on 8 July, 2011
- Releases b14 and b15 were private releases that I gave to a few people to test specific bug fixes. I incremented the release number to avoid confusion.
- It would be great if some of you could test the latest fixes--I've tested them, of course, but only on a few examples.
- I'd particularly appreciate if someone could test obo2obo to make sure my fix for [ geneontology-Bugs-3316815 ] (filtered save doesn't save dangling parents) didn't break anything in obo2obo.
- What would it take to make an official (rather than beta) release of OBO-Edit 2.1, so that people who are currently forced by work regulations to use OE 2.0 can officially switch over?
- Basically, someone needs to test and make sure that it saves everything properly. I *think* it does, but don't have a good way to make sure.
Fixed since last meeting
- filtered save doesn't save dangling parents
- Dangling parent save was broken (not by me) in r2703 on 5/14/2010. The change that broke it was these two lines that were added to OBOFileAdapter.doOperation (to fix the allowDangling behavior of obo2obo):
for(FilteredPath filteredPath : filteredPaths) filteredPath.setAllowDangling(ioprofile.allowDangling);
- Commenting out those lines fixed dangling save in OBO-Edit but broke it in obo2obo. My compromise fix is to propagate ioprofile's allowDangling setting to the filteredPaths only if ioprofile.allowDangling is true. This seems to work for both obo2obo and OBO-Edit for the cases I tried, but more testing would be good.
- (By the way, in debugging this, I discovered that the ioprofile that is passed to doOperation doesn't always seem to be the right ioprofile, and I'm surprised that this doesn't result in other incorrect parameter settings for load/save. Keep an eye out for issues that may be caused by the ioprofile being the wrong one.)
Currently working on
- beta 16 removing Xref and DBXref information
- Resulted from fixing a problem that was reported last month: Don't save dbxref lib description to obo file
- It was decided that we should have OBO-Edit save xref description for dbxrefs but NOT for definition xrefs.
- Future feature request: allow users to configure whether or not xref description is saved for dbxrefs and for definition xrefs.
- Is_a closure broken
- Terry wrote, "I just used beta14 to do is_a closure on cell.edit.obo with GO and PR. Overall it worked but there were two issues. 1) Non is_a relationships for previously MIREOTED terms were added, leading to a dangling parents error. For example, "regulates" relationships were added to many GO terms that were already in CL. 2nd, all typedefs disappeared."
- Midori commented, "I can confirm that I get the same thing (or at least something similar) happening with 'regulates' relationships: is_a closure saves some terms that would only be there if it followed at least one 'regulates' link. Curiously, it didn't include all 'regulates' links; the term I used for testing had a regulates link itself that apparently wasn't followed. Specifically, I tested using a nonsense xp in SO, with the GO term 'regulation of polysaccharide metabolic process' in an intersection_of tag. The saved file contained all the is_a ancestors I expected, plus the is_a ancestors of 'polysaccharide metabolic process' -- but it didn't have 'polysaccharide metabolic process' itself. I'm getting typedefs saved if they match the filter, and not if they don't (all are saved if I tick 'always save properties' - that seems to be working fine).
- Midori sent me a small example of the misbehavior--I haven't had a chance to test it yet.
Next bugs to work on (possibilities)
- problems with assert implied links panel
- The Assert Implied Links panel behaves badly in various ways. Will not be trivial to fix.
- Next OEWG meeting:
- Nomi will be away August 2--we'll skip that meeting.
- The next regularly scheduled OEWG meeting will be August 16
- Nomi summarised the talk she gave at the EBI on OBO-Edit fixes and future roles, and touching on the use of TermGenie.
- Protege as an alternative tool didn't meet with lots of enthusiasm (they like OE!) but people are willing to give it a go.
- The idea isn't to have one tool that does everything, but perhaps multiple tools that do something different.
- Heiko says to send suggestions for TermGenie to Heiko, cc-ing Chris Mungall. There will be a proper tracker in the future for recommendations.
- Jon Ison mentioned some features he'd like to see in OBO-Edit. He will send Nomi and Midori a message soon summarizing the features he described.