OEWG 20120501

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OBO-Edit Working Group Meeting: Tuesday, May 1, 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, Ramona, Paola

Bug and Feature Trackers

Fixed or newly added since last meeting

  • Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)
  • link filter not working properly
    • "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."
    • I broke this in 2.1.1-b7 as a side effect of fixing another bug: In compound ancestor/descendant queries, relation list bad
    • I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?

Currently working on

  • Cycle Check doesn't work
    • The Cycle Check verification check doesn't find cycles (tight or loose)
    • Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.
    • If this has been broken for that long, is it important to fix?
      • Ramona said that they have been having problems where there were cycles in their ontology that OE didn't catch and then when they loaded the ontology into Amigo, it complained. She thinks this is an important thing to fix.


  • Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.
    • I am not completely sure I interpreted the scenario correctly, as his description was brief.
    • He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.
    • I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.
    • I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.
    • There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.
  • I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)
    • Any other pressing bug fixes to get into this release?
  • Ramona mentioned that she sometimes pastes the wrong text into the text editor and tries Undo but instead of undoing her text edit, it undoes the last change she made to the ontology. She wishes she could just undo the last text change.
    • Nomi encouraged Ramona to submit a Feature Request for this, but said that the way the edit history is tracked, it would not be easy to add this kind of small-grained edits to the Undo history list. She suggested that Ramona try editing in Manual Commit mode instead of Autocommit mode if she wants to be able to discard unwanted text edits.


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