Protege 4.0 Alpha update (build 65)

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Protege 4.0 Alpha update (build 65)

Jennifer Vendetti
There is a new alpha build available on our Web site:

New features in the Protege-OWL editor
- Added finer control over the naming of new entities, including
automatic ID generation. This is described in more detail on the wiki [1].

- Created a wizard to selectively move axioms (Refactor | Move axioms to
ontology...). When multiple ontologies are loaded, there are several
strategies to select sets of axioms that can then be moved from one
ontology to another, e.g., move all disjoint axioms, move all axioms
referencing a certain class or classes, move all labels, etc.

- Implemented an action that removes all of the disjoint axioms that
reference subclasses of a selected class (Edit | Remove disjoints for

- Fixed and re-enabled the export of OWLViz diagrams to PNG and JPG.

- Changed the the default path to the dot executable for OWLViz on Mac
OS X to correspond to the current distribution

- Implemented a timestamp for debugging, accessible from Window |
Timestamp log/console.

- 64-bit Linux support for FaCT++ has been added.

Bug fixes for the Protege-OWL editor
- Fixed a bug that was causing DL queries to ignore changes in the
ontology since the previous classification.

- Fixed multiple rebuilds of rendering caches (therefore speeding
startup with large ontologies).

- The order of languages specified in the annotation renderer is now
correctly respected.

- Optimized the painting of most views (using framelists - such as the
Class Description) to speed up responsiveness.

- Corrected multiple bugs in the caches that caused old names for
entities to be retained in searches/expression editors and views to
ignore updates when the labels were changed (including the annoying bug
in trees where the new name got cut off if it was longer than the old name).

- Inherited anonymous classes pick up defined classes correctly (i.e.,
now shown for equivalent class axioms on ancestors).

- Reasoner errors should be more visible to users now. In particular,
Pellet now throws an exception if unsupported axioms are used in your
ontology (rather than silently stripping these out).

- Search now finds anything starting with the search string, regardless
of whether it is rendered with ' escapes (for names with spaces).

- It is now possible to cancel a close if ontologies are unsaved.

- Individual editors tidied up and now available for sameAs and
differentFrom assertions.

- Editing of disjoint axioms is now possible (and with a multiselect
tree or a comma separated list syntax, sets of classes/descriptions can
be added).

- Work has been done to ensure consistency between expression editors so
that they all use the same parsers.

- Multiple selection now reinstated for individuals (to allow deletion,

- Partially fixed a bug where OWLViz was failing to layout graphs when
accented characters were used in the names of things. Support for Latin
Extended A, Latin Extended B, and Korean characters was added. We would
appreciate feedback as to which other character sets should be supported
- in particular, if you are able to help us check that a particular set
works, that would be very useful.

- Changes to the ontology libraries are now saved when OKed and ignored
when cancelled.

- Selecting the location from which to load a new ontology no longer
ignores the user input when a bookmark is selected.

- Fixed "duplicate class" dialog exceptions on cancel.

- Look & feel options on the command line are no longer ignored.

- Ontologies menu cleaned up (including correct updates on ontology name

- A new version of the OWL API was bundled that fixes several Manchester
OWL Syntax issues.

As always, a Web-based version of the release notes is available on our
site [2].

The Protege Team


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