OEWG 20110920

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OBO-Edit Working Group Meeting: Tuesday, September 20, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Midori, Nomi, Paola, Heiko, Ramona, Laurel, Harold

Bug and Feature Trackers

Fixed since last meeting

Discussion Items

  • Have been looking through bug and feature trackers, closing some items, updating some, reprioritizing some.
    • All priority >=7 bugs have now been fixed
    • There are still a bunch of priority 7 feature requests
  • Why obo2obo fails some unit tests, and why it doesn't matter
    • The test involves using OBO2OBO to roundtrip test_resources/testfile.1.0.obo and then to convert it to obo1.2 format, and to check that there are no significant differences.
    • It finds lots of differences, but I determined that they all fall into one of the following categories:
      • The use of "xref_analog" instead of "xref" (the testfile uses xref; the new output has xref_analog instead), e.g.,
< xref: TC:2.A.5.1.1
---
> xref_analog: TC:2.A.5.1.1
      • The (agreed-upon) elimination of database descriptions from definition and synonym dbxrefs, e.g.,
< def: "The process by which a phagosome, a vesicle formed by phagocytosis, fuses with a lysosome." [GOC:add, ISBN:0781735149 "Fundamental Immunology"]
---
> def: "The process by which a phagosome, a vesicle formed by phagocytosis, fuses with a lysosome." [GOC:add, ISBN:0781735149]
< related_synonym: "baroreceptor pressure buffer system" [ISBN:068340007X "Stedman's Medical Dictionary"]
---
> related_synonym: "baroreceptor pressure buffer system" [ISBN:068340007X]
      • The new version backslashes special characters like "," in xref_analogs, e.g.,
< xref_analog: MetaCyc:(R,R)-BUTANEDIOL-DEHYDROGENASE-RXN
---
> xref_analog: MetaCyc:(R\,R)-BUTANEDIOL-DEHYDROGENASE-RXN

(I'm not sure when or why that change was made but I assume it was requested.)

      • And that's it--everything else is roundtripping as expected.

I think it would be more trouble than it's worth to fix these (and other) tests to return success, but I feel reassured (and I hope you do, as well) that OBO2OBO is working as correctly as ever.

  • Is_a closure broken
    • This is behaving better than it used to, but it is not completely fixed. It now saves all the desired is_a ancestors but also includes a few terms that aren't is_a ancestors.
    • I have already spent too much time on this--I'm going to put this one aside for now. Priority lowered from 7 to 6.
    • Chris said "This has become a lower priority for OE, since we will be able to do most of this in Oort."
      • Heiko will talk to Chris about sending out a message about Oort
  • No longer offering Linux RPM installer
    • Heiko discovered that if you use this, it doesn't set the memory allocation for OE--OE would launch with the (low) default java memory setting, which is not enough to do anything interesting.
    • Rather than spend a lot of time catering to this fringe market, we will no longer offer the Linux-specific installer. Linux users can use the generic Unix installer (which, presumably, many of them already were).
  • Allow 64 bit to be chosen on install
    • Heiko has found a way to make the installer detect whether you have a 64-bit machine and 64-bit java, and if so, it suggests a higher memory setting.
    • We are still testing this (looking for volunteers).
    • We added to the user guide explanations about memory settings and how to make your Mac boot in 64-bit mode.
  • Harold: some ontology someone's working on still looks weird in OE 2 (terms showing up as roots that shouldn't be roots), although it looks ok in OE 1. (GO looks basically the same in OE1 and OE2.)
    • Harold agrees that the ontology in question is buggy. He will send it to Nomi, but agrees with her that she shouldn't spend a lot of time trying to get OE2 to display a buggy ontology in the desired way.

Currently working on

  • Working towards making an official 2.1 release

Next bugs to work on

  • Last chance to nominate your "favorite" bugs...

Links

Back to OEWG meeting agenda and minutes list