Protege 3.4 Beta update (build 500)

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Protege 3.4 Beta update (build 500)

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

http://protege.stanford.edu/download/prerelease/full/
http://protege.stanford.edu/download/prerelease/basic/

IMPORTANT - PLEASE READ: This beta build is a major change from the
previous build (build #130) and is likely to have some initial problems
because there is so much new functionality.  So - save your work before
trying this build, don't use if for mission critical applications  ;) , etc.

The motivation for such major changes is that we have made three
significant improvements that have been requested for a long time:

1. Database Inclusion - Until now, database inclusion has not been
available in Protege.  This has led to many workarounds and
inconveniences for users who want to work with ontologies in a database
mode.  For users who are ready to try this functionality out, we have
written a web page [1] describing how to use the database inclusion
mechanism. Note that there has been an incompatible change in the
database format. You will not be able to use existing database projects
- you will need to use a pre-build 130 version of Protege to convert the
database project to an owl project first and then convert it with the
new build to a database project.

2. New Protege-OWL Parser - The previous version of the Protege-OWL
parser had many problems that made it perform badly, use lots of memory
and be fragile. The new parser is much more robust, uses significantly
less memory, is much faster and has a better support for untyped resources.

3. Decoupled Namespace Management - There have been several complaints
about the way that Protege handles namespaces.  For example, users have
requested better URN support and a decoupling of the name of the
xml:base, ontology name and the default namespace. In previous versions
of Protege, the namespace code was tightly coupled with the underlying
owl model.  This led to many quirks in the way that Protege behaved.  
Now the namespace management code is a thin layer which defines how the
ontology is presented to the user.  This build provides better URN
support and better xml:base, ontology name and default namespaces
decoupling.

Known Incompatibilities

1. The database schema used by the database backend has changed in an
incompatible way.  An existing database project will need to be
converted to a file based project before it can be used with this
version of Protege. This means that to use an existing database with the
new build, you will have to first convert it to a file using the menu
File -> Convert project to format. And then, open the converted file
project with the new build and convert it back to a database format.

2. For OWL projects, the format of  the .pprj file has changed in an
incompatible manner.  The new version of Protege will be able to read
existing .pprj files but when these files are saved they will not be
properly understood by previous versions of Protege.

3. Another important change is that the internal names of the ontology
entities are now the fully qualified name, rather than the prefixed
name. This may impact application developers. It is recommended to adapt
your code to use the full name. The short name is still supported, but
may have a performance impact. The support for short names can be
disabled, by setting in the protege.properties file the property
owlmodel.expand.short.name.in.methods to false. The class
edu.stanford.smi.protegex.owl.model.NamespaceUtil provides conversion
methods between the full and short names of ontology entities. If you
are developing a user interface, then it is recommended that you display
the browser text of an entity, which shows the prefixed name.

3. Although we tried to test as many plug-ins as possible, some plug-ins
may need to be adapted to the new build. If you notice any plug-ins
misbehaving, please report them on the protege mailing list.

4. If you have existing Collaborative Protege projects in OWL, you will
not see the annotations attached to the ontology components anymore,
because the name of the entities in the annotation ontology used to be
the short name, rather than the long name. We will provide shortly a
conversion routine that will adapt existing annotation projects to use
the full name of entities.

Best Regards,
The Protege Team

[1]
http://protegewiki.stanford.edu/index.php/Working_with_the_Database_Backend_in_OWL

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