OBO-Edit Working Group Meeting: Tuesday, September 20, 2011, 8:30am PDT
Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
Agenda/Chair: Nomi Harris
Attendees: Midori, Nomi, Paola, Heiko, Ramona, Laurel, Harold
Bug and Feature Trackers
Fixed since last meeting
- Extended Characters not being caught
- Since the "Allow extended characters" configuration option wasn't working, I have disabled it for now. The current treatment of extended characters (permitted in synonyms, definitions, and comments; not permitted in dbxrefs) is what most people want anyway.
- Turned off repeated whitespace check by default
- history browser won't save history
- Turned out to be a simple fix (was throwing an exception).
- Verification plugin should flag synonyms that match term
- 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.
- Are these two Feature Requests now working? If not, need examples.
- 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...