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2.1-b11 released on 3/24/2011

Bugs Fixed

  • Words added to dictionary in unedited term don't turn black immediately
    • If you are editing a term and OBO-Edit colors a word red because it thinks it's misspelled, you can add the word to the dictionary and then it turns black. However, if you loaded an ontology and there were words that OBO-Edit didn't recognize, adding them to the dictionary didn't make them turn black right away. Now fixed.
  • explanation component not working
    • The Explanations component and Graph Editor weren't showing explanations for some newer explanation types (just the question, "Why is this link in the ontology?"). Now they show raw explanations for any explanation types that don't have a pretty form defined.


  • Made Configuration manager window a bit bigger so nothing is cut off.
  • Not all the "Show warnings" checkboxes were visible with the Verification Manager its normal size--one was hidden. Made labels shorter so they all fit.
  • Repeated word warnings: was warning about some repeated digits (e.g., "7.7-dimethyl-whatever"). Now all of the digits are in the allowed-repeats list.
  • Changed max number of warnings to show from 200(ish) to 300(ish).
  • Added info to user guide on how to save an ontology that has fatal errors.

Future Work

  • Is_a closure broken
    • Broke some time between 2.1-b4 and 2.1-b9?
  • merge sometimes loses text details; sometimes can't undo merge
    • Sporadic and not new to 2.1b10
    • I have not been able to reproduce either problem. Midori and Ramona have both seen the loss of information on merge, but couldn't reproduce it reliably. Midori has found that sometimes she can't undo a merge, but it's unclear when/why that happens.
    • If anyone can give me a repeatable example of these problems, I will do my best to track them down.
  • Bad handling of unrecognized relation (text editor et al.)
    • I looked into this some--will not be simple to fix. Has to do with how dangling objects (e.g., unrecognized relations) are handled in different components.
  • Terry says when you run the reasoner it gives you a line indicating an error/warning, but not an answer about why the relationship is wrong. Nomi suggested he submit a bug report on high priority.


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