OEWG 20120703

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OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT

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

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori

Bug and Feature Trackers

Fixed or newly added since last meeting

  • Cycle Check doesn't work
    • New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.
    • The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.
    • The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.
  • Name redundancy check not working in Text Editor
    • It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).

Current work

  • Custom dictionaries
    • OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.
    • Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)
    • Nomi started working on this; Heiko will finish it.


  • Important announcement from Nomi: as of July 1, she has a new job (and thus will no longer be working on OBO-Edit). Nomi is now the program manager for KBase, a knowledgebase for predictive biology. (The project is based at LBNL, but in a different division.)
    • Heiko will take over as the OBO-Edit support person, but will only fix showstopper bugs--most of his time is spent working on next-generation ontology tools.
    • Heiko and Chris will continue to hold an OEWG meeting on the first Tuesday of each month, but it will become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)

  • Released OBO-Edit 2.2 on May 24 (I was going to call it 2.1.1 but decided that was too confusing)
    • Passes the usual unit tests
    • Mike Cherry tested it in the pipeline and said it seemed fine
    • Several OEWG members said that it works for them
  • Most important unfixed bug: problem on some Windows 7 computers
    • Hard to attack this one when the people who report it won't give us any additional info, and no one in the OEWG has ever observed it themselves.
  • Ramona reviewed her bug reports and feature requests and updated priorities
  • Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."
    • Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.


Back to OEWG meeting agenda and minutes list