OEWG 20120807

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OBO-Edit Working Group Meeting: Tuesday, August 7, 2012, 8:30am PDT

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

Agenda/Chair: Heiko Dietze
Attendees: Heiko, Midori, Ramona, Chris, Paola, Becky

Goal of this meeting: Extend the scope of this call to become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)

Some open questions:

  • Do we need a new name?
 Not for now, but change the description of the list. Renaming of lists on source forge is not possible. We would have to create a new one and everyone had to subscribe again.
  • Where to announce the meetings (currently its the OBO-Edit working group mailing list)?
 Announce the new scope (and that there is such a call) on OBO-Discuss or may be even on the GO list to reach a broader audience. Regular updates on the original list.
  • Who is the targeted audience?
 Help on the path and transition to OWL. OWL users with a background or use case in OBO.

Bug and Feature Trackers


Fixed or newly added since last meeting

The main improvement is the option to add more dictionaries for the spell-checking. This will allow enable users to share dictionaries (e.g., in an SVN) without the need to copy and overwrite them manually in the OBO-Edit configuration folder.

Currently working on

  • Testing of the new dictionary feature (EBI GO Editors - nothing to report yet)
  • Integrate the latest bug-fixes of the obo2owl and owl2obo conversion into OBO-Edit (ongoing)

Recent Bug Reports

  • Reporting of errors in imported ontologies is insufficient
  • Vanishing ontology, after using any key (e.g. typing for search, press ALT or CTRL):
    • Bug reports: report 3, report 2, report 1
    • I could now reproduce the problem and found a bug fix for the problem. In general there was an issue while checking for Mnemonics (e.g. CTRL + O for load ontology). Due to the bug, any key stroke resulted in a call to 'New Ontology', which is the first menu item.
    • This will be fixed in the next beta (b2).
    • Work around until the new release: use Java 6

OBO Format

  • OBO writer: Fixed a bug for the property value writing
  • SPEC: Updated spec, TODO move or copy the recommended tag order for serialization from OBO format guide 1.4 to specification
  • OWL2OBO: new CLI option to write untranslated axioms into a file


  • OORT: per Davids request there is a new ontology file, which contains the same as the main ontology (MIREOT + asserted inferences), but removed the equivalence axioms. Current (intermediate?) name: 'relaxed'
  • ELK 0.3.0 support: Due to a bug in the current 0.3.0 release this is delayed. bug report Yevgeny already has fixed the bug and its available in the nightly builds. Nightly builds are available from: http://code.google.com/p/elk-reasoner/wiki/GettingElk


MIREOT vs OWL imports (Midori, Ramona, Chris)

  • MIREOT intended for OBO-Edit; Draw back: possible errors by hand editing (copy and paste) of new terms, which are not yet MIREOTed into the ontology.
  • Full (OWL) imports might have a negative performance impact.