Protege 4.0 Beta update (build 107)

There is a new Protege 4.0 beta build available on our Web site:

http://protege.stanford.edu/download/registered.html#p4


Enhancements in Protege-OWL
---------------------------------
- A Beanshell plug-in is now available [1] that allows users to write 
scripts to interact with the model/user interface from within Protege-OWL.

- A Manchester syntax view is now available (shows the current selected 
entity), which is good for easy cut and paste into emails.

- Refactor | Copy/move/delete axioms... has been revisited such that you 
can select axioms by profile, e.g., EL++, and it is also now pluggable.

- There is a new Individuals by inferred type view.

- Load errors for some formats now provide more help with line numbers 
and allow you to view the sources.

- It is now possible to save as OBO 1.2 flat file format. This feature 
should be used with care. In particular:

1) Not everything in OWL can be represented in OBO format. Warnings are 
currently only reported to the console so please have this open when 
using this feature.
2) This was written using incomplete OBO documentation. We expect bugs 
and omissions and are interested in user feedback, so please try it and 
let us know what you think.

- There are several OWLViz updates:

1) Some global preferences have been moved into the File | Preferences | 
OWLViz menu.
2) Tracking view: OWLViz views (including plug-ins such as OWLPropViz) 
now allow a tracking mode which follows the current selection:

  a) You can select the default mode for all OWLViz views in File | 
Preferences | OWLViz.
  b) Some views allow you to turn this on/off locally using the view's 
Options button and selecting the Mode tab.
  c) "Track selection" means that the global selection will be followed 
in OWLViz, making it good for using it as a navigation tool.
  d) "Create graph manually" is the default behaviour, where you tell 
OWLViz which classes to show using the toolbar.
  e) Providing a radius tells OWLViz how many classes around the current 
selection you wish to see.
   
3) Inferred view: nothing is only displayed as a subclass of Thing (no 
longer all classes making the view hard to read).

- Rename entity has been renamed (!) to "Change entity URI...".

- Change entity URI... allows you to select whether you wish to also 
rename puns.

- DL Query now provides result counts.

- Individuals by class view now gives membership counts.

- Custom tab layouts can now be removed.

- The changes plug-in has been updated to provide a simple axiom diff 
view to see the difference between two loaded ontologies. Note that this 
plug-in must be downloaded separately [2].


Bug Fixes in Protege-OWL
----------------------------
- Fixed a bug where an exception was raised if searching for datatypes.

- Fixed a bug where FaCT++ was not returning inferred domain and range 
information.

- Fixed a bug where an exception was being thrown when trying to accept 
auto-updates.

- Fixed a bug where it was possible to add multiple prefixes with the 
same name.

- Fixed a bug in the class hierarchy that was causing gaps to appear in 
the tree after drag and drop.

- Fixed a bug in the class hierarchy where selection failed in some 
circumstances.

- Individuals on the "Individuals by Class" tab are now sorted.

- dataOneOf now works in the expression editors.

- owl:Nothing and other unsatisfiable classes are now hidden in DL query 
results.

- owl:deprecated was added to standard annotation URIs.

- The export format can now be selected when saving inferred axioms.

- Local/web imports are now added to the recent locations list.


As always, a Web-based version of the release notes is available on our 
site [3].

The Protege Team

[1] http://code.google.com/p/co-ode-owl-plugins/wiki/BeanshellView
[2] http://code.google.com/p/co-ode-owl-plugins/wiki/ChangeView
[3] http://protege.stanford.edu/download/protege4/release-notes.html

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