OEWG 20110830

OBO-Edit Working Group Meeting: Tuesday, August 30, 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

• OE Bug tracker
• OE Feature tracker

Fixed since last meeting

• Heiko replaced the File Browser in OE with the native one so that you have the full browsing power of the Finder (and it remembers where you last browsed, which is also great). This is a fix for File browser in Mac OBO-Edit doesn't show second hard drive. The one small downside of the new File Browser is that you can't load multiple files at once (from the Basic Load interface), but OE users said that was ok, they didn't load multiple ontologies that way anyway (those who load multiple ontologies at once prefer to use the Advanced load with saved load profiles).
• Name Redundancy check doesn't work
  • Jane wrote, "I managed to commit two terms to GO which had identical names to existing terms this week, without the verification plugin objecting."
  • Nomi and Midori both tested the Name Redundancy check and it worked for them.
  • Karen C. said, "I have just checked the Verification Manager settings and the check boxes for "On text commit?, "On save?", and "On manual?" are ticked. However, I don't recall having been warned in either case. I could easily have overlooked the "On save" warning as I become blase about reading those since there are always 30 or so of those, but I did try to skim through and see if there was anything new. However, I do not recall getting a warning when I committed this term."
  • Clarification from Midori: the redundant name warning appears in the Verification Manager but doesn't appear as a popup (I didn't realize it ever did). I will fix that. Are there other warnings that used to appear as popups that now don't? I don't want to make all the warnings popups because that's annoying.
• obo2obo no longer prints status messages to stdout

Discussion Items

• New file browser had bug in b17--Heiko quickly fixed it and we released b18 the next day.
• Did anyone (other than Midori) get a chance to test obo2obo to make sure my fix for [ geneontology-Bugs-3316815 ] (filtered save doesn't save dangling parents) didn't break anything in obo2obo?
  • Midori found one issue in obo2obo but it turned out to be old and unimportant
  • Fixed problem where obo2obo recently stopped printing status messages to stdout.
  • The obo2obo tests I tried yielded the same output for OE 2.0 and 2.1-b18.

• Next meeting: we will skip Tuesday, September 6 and meet next on September 20.
• With a new academic year starting, should we revisit the meeting day/time or just keep it as it is?

Currently working on

• Working towards making an official 2.1 release
  • Trying to get JUnit tests working again (for OBO and OBO-Edit) and make sure that current OE behavior is no worse than the behavior of 2.0.
• 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).

Next bugs to work on

• Fixing JUnit tests for OBO and OBO-Edit
• Fixing any bugs that the JUnit tests reveal

Discussion

Links

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