readme.txt

August 7, 2006 · View on GitHub

SWOOP v2.3 beta 3 Release Date: January 4, 2006

Organization: MINDSWAP (http://www.mindswap.org), University of Maryland, College Park Supervisor: Professor James Hendler (hendler@cs.umd.edu) Project site: http://www.mindswap.org/2004/SWOOP Mailing Lists: http://lists.mindswap.org/mailman/listinfo/swoop (users), http://lists.mindswap.org/mailman/listinfo/swoop-devel (developers)

Primary Developers (in alphabetical order): Aditya Kalyanpur (aditya@cs.umd.edu) Bijan Parsia (bparsia@isr.umd.edu) Evren Sirin (evren@cs.umd.edu)

Other Contributors (in alphabetical order): Bernardo Cuenca Grau (bernardo@mindlab.umd.edu) Daniel Hewlett (dhewlett@umd.edu) Michael Grove (mhgrove@hotmail.com) Ron Alford (ronwalf@wam.umd.edu) Taowei David Wang (tw7@cs.umd.edu) Vladimir Kolovski (kolovski@cs.umd.edu)

Installation Instructions: After unzipping the downloaded file (SWOOP-xxxx.zip), execute runme.bat (/ runme.sh) present inside the "SWOOP-xxxx" directory to start the application on a Windows (/ Mac or Unix) machine. For loading large ontologies such as NCI, you need to allocate more memory for Swoop - use the runme-HIGH file in this case.

***** Important Notes: *****

The application requires Java 1.4 installed on your machine. You can download the latest version of Java from http://java.sun.com/j2se/1.4/download.html
The SWOOP application includes/uses the following API's: ** WonderWeb OWL API (http://sourceforge.net/projects/owlapi) MODIFIED SOURCE (see changelog at the end of source file) ** XNGR API (http://xngr.org/) ** Jakarta Slide WebDAV API (http://jakarta.apache.org/slide/) ** QTag API(http://www.english.bham.ac.uk/staff/omason/software/qtag.html) developed by Oliver Mason, whom we thank for allowing us to bundle qtag.jar with this Swoop release (please see licensing.txt for more information about its use) ** Hexidec Ekit API (http://www.hexidec.com/ekit.php) MODIFIED SOURCE (see changelog at the end of source file) which are located in the /lib sub-directory under SWOOP. Additional jars in the lib directory (if present) are plugin dependencies.
SWOOP employs a plugin based system for easy extension. Sample plugins can be downloaded from http://www.mindswap.org/2004/SWOOP/plugins

Software Description:

SWOOP is an OWL Ontology browser/editor that takes the standard Web browser as the basic UI paradigm. Swoop includes many of the familiar features of a Web browser such as an address bar and history buttons, bookmarks, hypertextual navigation etc. and applies them to the problem of browsing and editing Web based ontologies. Features include:

It is simple to load ontologies from the web and to navigate within and between them.
Multiple ontologies may be loaded at the same time.
Ontologies, classes, properties, and individuals are rendered in a high level, accessible manner.
One can "view the source" of ontologies and their entities in a number of common syntaxes (e.g. RDF/XML, the OWL Abstract Syntax, Turtle).
OWL reasoners can be integrated for subsumption, consistency checking etc. -- default reasoners include a RDFS-like simple reasoner and Pellet, a Description Logic Tableaux Reasoner.
Ontology change management with extensive rollback and undo mechanisms
Share Annotations on Ontologies using the Annotea Protocol. Also attach and distribute Ontology Change sets with Annotations
Search across multiple ontologies and 'find all references' of an OWL named entity
Compare entities using a Resource Holder
Export Ontologies directly to a remote WebDav store

This version contains some advanced, experimental features such as:

Debug Ontologies using Pellet (explanations for unsatisfiable classes & inconsistent ontologies)
Run "sound and complete" conjunctive ABox queries (written in RDQL) on an ontology using Pellet
Partition Ontologies automatically by transforming them into an E-connection
Crop Circles visualization of class hierarchy

New Features in v2.3 beta 3:

Ability to edit entities in Turtle Syntax, Abstract Syntax and RDF/XML with ontology changes logged as well
Support explanation of inferences for complex ontologies such as Wine, Pizza, Galen etc.
Ability to generate and export HTML for an Ontology, Class, Property or Individual based on current selection in display
Plugin for "Natural Language" Rendering of OWL Entities included
Ability to Auto-Save Workspace at regular intervals
Numerous improvements to the CropCircles UI

Bugs fixed since previous version:

ABox Query (missing jar) fixed
Fixed problem due to removal of instances
Fixed hasValue restriction on datatype properties
Made component-names consistent across UI
Fixed problem with cancellation of progress bar when reasoning with Pellet

New Features in v2.3 beta 2:

Entities can be displayed using either their URIs or their rdfs:label or in a particular language when xml:lang is used in the rdfs:label (see option in File->Preferences)
Ability to sort and remove Bookmarks
Ability to set an HTTP proxy server host/port when using Swoop behind a firewall
Progress bar displayed when shifting to Pellet reasoner
Explanation of inference improved: strikes out irrevelant parts of axioms
"Save Ontology" menu option label changes when associated with an ontology

Bugs fixed since previous version:

Renaming OWL Entities works properly now
Axiom tracing catches more axioms (new version of pellet-debug.jar included)
Version Control update/commit to repository works properly now
Overwrite prompt appears only when file exists and trying to save file
Fixed some RDF/XML serialization bugs (e.g. xml:lang instead of rdf:language)
Fixed errors in tree statistics in Swoop OntologyInfo pane

New Features in v2.3 beta 1:

Latest version of Pellet 1.3 for reasoning..handles large, complex ontologies such as Wine, Galen, Pizza etc.
Explanation support for inferences when Pellet is turned on (see "Why?" link next to italicized assertion)
Version control using Annotea (see menu option: Advanced->Version Control)
Support for adding arbitrary class expressions
Support for viewing, creating and deleting GCIs in the ontology (see "Show GCIs" option for alphabetical list)
Advanced Ontology Statistics pane

Bugs fixed since previous versions:

Bookmarks now work properly for local files as well
Anonymous individuals now appear in the alphabetical list ("Show Individuals")
Warning message displayed when overwriting a saved ontology file

Key known issues in last stable release v2.2.1:

The ontology (class/property) JTrees are cached after classification of the ontology using the reasoner. But the reasoner results themselves are not cached. This makes switching between ontologies when Pellet is ON considerably slow.
No form-based UI to create/edit nested Class Expressions. The workaround for now is to edit these in the RDF/XML inline tab.
If the size of the logged changes in SWOOP becomes large, rendering them takes time because of a bug in the implementation. A workaround for now is either: Save the ontology/workspace as a SWOOP file (*.swo, *.swp) which saves all the changes. Then remove portions of the change log (see "Remove" link in logpane) and resume editing; OR Disable change logging (File->Preferences) and/or turn off change rendering altogether ("Show Changes" checkbox).
No RDF/XML rendering of datatype enumerations supported (e.g. NATO ontology in the default bookmarks cannot be serialized)
"Show References" method does not consider imported ontology information.

For other, less critical issues see: http://www.mindswap.org/issues/