OEWG 20110830

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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

Fixed since last meeting

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

Back to OEWG meeting agenda and minutes list