OEWG 20120807: Difference between revisions

Revision as of 11:22, 7 August 2012

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:

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?
Where to announce the meetings (currently its the OBO-Edit working group mailing list)?
Who is the targeted audience?

Bug and Feature Trackers

OBO-Edit

Fixed or newly added since last meeting

Beta-Release: 2.3-beta 1.

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 (Paola)
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
- Bug Report

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 serilazation from OBO format guide 1.4 to specification
OWL2OBO: new CLI option to write untranslated axioms into a file

OWLTools

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. Currently testing.

@@ Line 40: / Line 40: @@
 * Vanishing ontology, after using any key (e.g. typing for search, press ALT or CTRL):
 ** Bug reports: [http://sourceforge.net/tracker/?func=detail&aid=3534554&group_id=36855&atid=418257 report 3], [http://sourceforge.net/tracker/?func=detail&aid=3523730&group_id=36855&atid=418257 report 2], [http://sourceforge.net/tracker/index.php?func=detail&aid=3495346&group_id=36855&atid=418257 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 [http://en.wikipedia.org/wiki/Mnemonics_%28keyboard%29 Mnemonics] (e.g. CTRL + O for load ontology). Due to the bug any stroke resulted in a call to 'New Ontology', which is the first menu item.
+** I could now reproduce the problem and found a bug fix for the problem. In general there was an issue while checking for [http://en.wikipedia.org/wiki/Mnemonics_%28keyboard%29 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 ==