Projects

neon-toolkit

The aim of the NeOn (Networked Ontologies) project is to advance the state of the art in using ontologies for large-scale semantic applications in the distributed organizations. .

neon-plugins

The aim of the NeOn (Networked Ontologies) project is to advance the state of the art in using ontologies for large-scale semantic applications in the distributed organizations. Particularly, we aim at improving the capability to handle multiple networked ontologies that exist in a particular ... [More] context, are created collaboratively, and might be highly dynamic and constantly evolving. This project covers the plugins for NeOn core. [Less]

BioPAX

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. The goal of the BioPAX group is to develop a common exchange format for biological pathways data. The BioPAX project began at the Fourth BioPathways Consortium Meeting, a satellite of the ISMB'02 ... [More] Conference held in Edmonton, Canada in August 2002. It was decided that a pathway exchange format would facilitate sharing of pathway information between databases and users and would be a good first step to building an open source pathway information resource. The project got underway in early October 2002 when Chris Hogue (BIND, UToronto), Peter Karp (BioCyc, SRI), and Chris Sander (MSKCC) organized the BioPAX work group. [Less]

semanticturkey

Semantic TurkeyA Firefox Semantic Bookmarking and Annotation ExtensionSemantic Turkey is a platform for Semantic Bookmarking and Ontology Development realized by the ART Research Group at the University of Rome, Tor Vergata By adopting W3C standards for knowledge representation, such as RDF, RDFS ... [More] and OWL, Semantic Turkey turns the popular Web Browser Firefox into a rich and extensible framework for knowledge acquisition, management and exchange. Users can adopt Semantic Turkey to keep track of relevant information from visited web sites and organize collected content according to imported/personally edited ontologies. Domain experts and ontology developers can now build ontologies starting from the very raw source of information which they find on the web, without any need of interconnecting different heterogeneous tools and applications Semantic Turkey is built on top of several different technologies such as Java and Javascript, XUL, XBL, and features a three layered (data, business and interaction models) architecture, exploiting the AJAX paradigm for UI/Business logic communication. By exploiting acclaimed modularization frameworks such as OSGi compliant Apache Felix and the Mozilla extension environment, Semantic Turkey can be easily extended with new plug'n'play applications, embracing the best of both worlds of Knowledge Engineering and Web Browsing. Depending on their needs, extension developers can thus rely on different RDF management libraries, such as Sesame or Jena, as well as reuse and integrate functionalities from the full range of extensions in the Firefox Add-ons repository The three Web SitesThis is the project site of Semantic Turkey, containing source code, bug reports etc... If you have stumbled upon this site for the first time, we recommend first to visit Semantic Turkey main site, which contains useful information such as installation requirements, documentation etc... ...and if you don't like manuals, please give at least a look to the requirements section of the main site, to know what you need for running Semantic Turkey! :-) To install Semantic Turkey, visit the Semantic Turkey Firefox extension page to download its xpi (Cross-Platform Installer) package (again, read the requirements section before downloading it). [Less]

owlviz

OWLViz is a hierarchical visualisation system for OWL ontologies.

visuowl

VisuOWL Version 0.2 VisuOWL is a Java/Swing application for the visualisation and browsing of entities in OWL models and the relations between them. It uses the OWL API for the manipulation of OWL files and Jgraph Layout Pro for displaying the networks. FEATURES Visualisation of entities of ... [More] OWL models. Searching for an entity, visualise its neighbours and navigate in the network, starting from there Filter the types of relations Change the graph layout CONTENTS visual.jar: binaries of the program src: source code idiomas.csv: languages file (also included in the jar) REQUIREMENTS Java 6 OWL API (owlapi-bin.jar): downloadable from http://owlapi.sourceforge.net JGraph Layout Pro (jgraphlayout.jar): obtained from http://www.jgraph.com. Free, only for academical purposes. Several OWL files might also need xercesImpl.jar All the above jars are included in the classpath, in the MANIFEST.MF inside visuowl.jar USAGE java -jar visuowl.jar (with the required jars in the same directory) SCREENSHOT KNOWN ISSUES Big graphs are not always completely visible. The user has to maximise the window and use the scroll bars. When layout changes the window minimises. No memory for very big OWL models (try running with a bigger heap size: -Xmx512M or higher) Expansion is possible but its inverse is not Developed and supported Hugo Gonçalo Oliveira, hroliv(a)dei.uc.pt [Less]

O-DEVICE

O-DEVICE is a CLIPS-based production rule OWL reasoner that maps OWL ontologies on the Object-Oriented language of CLIPS, namely COOL. Furthermore, JO-DEVICE is available that enables O-DEVICE to be used in JAVA applications.

visegraph

ViSeGraphViSeGraph, formerly known as VisuOWL, is a Java/Swing application for the visualisation and browsing of entities in OWL models and the relations between them. It uses the OWL API for the manipulation of OWL files and Jgraph Layout Pro for displaying the networks. FEATURES Visualisation ... [More] of entities of OWL models. Searching for an entity, visualise its neighbours and navigate in the network, starting from there Filter the types of relations Change the graph layout CONTENTS visuowl.jar: binaries of the program src: source code idiomas.csv: languages file (also included in the jar) REQUIREMENTS Java 6 OWL API (owlapi-bin.jar): downloadable from http://owlapi.sourceforge.net JGraph Layout Pro (jgraphlayout.jar): obtained from http://www.jgraph.com. Free, only for academical purposes. Several OWL files might also need xercesImpl.jar All the above jars are included in the classpath, in the MANIFEST.MF inside visuowl.jar USAGE java -jar visuowl.jar (with the required jars in the same directory) SCREENSHOT KNOWN ISSUES Big graphs are not always completely visible. The user has to maximise the window and use the scroll bars. When layout changes the window minimises. No memory for very big OWL models (try running with a bigger heap size: -Xmx512M or higher) Expansion is possible but its inverse is not Developed and supported Hugo Gonçalo Oliveira, hroliv(a)dei.uc.pt [Less]

co-ode-owl-plugins

OWL plugins for the Protege 4.0 ontology development platform, created by members of the CO-ODE team and other associates at the University of Manchester. Installation instructions. Please make sure you backup regularly PluginDescriptionSince OBO ToolsA selection of tools for OBO ... [More] ontologies.build 112 URI ToolsSimply display the URI of the selected entity.build 109 OWL Calculations pluginSupport for arithmetic computation in OWL.build 59 OPPL (Ontology Pre-Processing Language)Support for transformations in OWL.build 101 OPPL PatternsSupport for patterns in OWL.build 110 Beanshell ViewDirect access to P4 through a scripting tab.build 103 SKOSedView and edit SKOS vocabularies.build 104 Change ViewA useful debugging tool that shows all changes to the model since startup.build 62 Annotation Template ViewAn easy to edit metadata set.build 61 Annotation SearchFind/filter/text search annotations across all active ontologies.build 62 OWL lintSupport for a test framework for OWL.build 59 TerMineExtract candidate terms from a corpus.build 59 OWLDocJavaDoc style HTML export and view for your ontology.build 57 Outline/Existential TreeViews tracing down existential hierarchies for given properties.build 62 Taxonomy cut+pasteTwo example plugins for showing class descendants for pasting into documentationbuild 57 Cardinality ViewAlternative (cardinality focused) restrictions view for OWL classesbuild 57 BookmarksA list of useful classes/properties, saved with your ontology.build 57 Cloud ViewsClass/Property browsing by various measures of "importance".build 57 Excel ImportCreate class descriptions from excel tables.build 61 MatrixTabular views of classes, properties and individuals.build 57 DL QueryGet sub/superclasses of arbitrary class descriptions.build 57 OWLVizGraph view of the ontology.build 57 The NerdThe Protégé version of "Clippy" that everyone loves to hate.build 57 Funded by JISC. [Less]

ontology-browser

Tired with having to produce loads of static HTML using OWLDoc and then having to upload it to your server? The ontology browser allows you to navigate around your ontologies in the same familiar environment, but produces the pages dynamically and is available for direct use with a web front-end. ... [More] Try it here by loading one of your own online ontologies or Browse the pizza ontology or add a link on your own pages to your ontology: http://owl.cs.manchester.ac.uk/browser/manage/?action=load&clear=true&uri=http://www.example.org/ontology.owlDocumentationGetting started with the ontology browser Release Notes Instructions for installing the browser on your own server (or locally). FeaturesFull OWLDoc entity renderings dynamically created on the fly All pages navigable by links Fully indexed ontologies, split down by module and entity type Partial, expandable class hierarchy shown Find entities by name with autocomplete Tag cloud views of class/property usage DL queries using full Manchester Syntax Permalinking (at bottom of each page) for sharing pages with friends REST API with xml/html results (work in progress) utf8 encoding Level of SupportAs with most new software, things are changing rapidly, so we do not have the resources to actively support the server. AcknowledgementsThis work is funded by JISC. We work in collaboration with partners from Stanford University and other institutions in the UK. Copyright © 2007 The University Of Manchester [Less]