Ontology

Docgen plugin for Protege provides a quick export of all the content of an ontology (classes, instances and documentation) in various formats (html, pdf, fo...). Images, Graphs, URL are readyly included in reports. Platforms: Windows, Mac, Linux

Dogwood is an ontology-aware Distributed Annotation System (DAS) server framework for the integration of biological, biomedical and clinical data. Platforms: Windows, Mac, Linux

Hawthorn provides a caching and lookup mechanism for bioinformatics ontology formats such as OBO and DAG. Platforms: Windows, Mac, Linux

HERAKLES is a reasoning broker framework for OWL (Web Ontology Language) reasoning systems. Platforms: Windows, Mac, Linux

MapPSO is a tool for Ontology Alignment, which uses Discrete Particle Swarm Optimisation. A particle swarm is used to search for the optimal alignment. The algorithm is massively parallel and adapts naturally on parallel architectures. Platforms: Windows, Mac, Linux

OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses. Platforms: Windows, Mac, Linux

Ontology visualization plugin for Protege in an interactive 3D space. Platforms: Windows, Mac, Linux

OSGI4AMI Ontology (http://www.booksonline.iospress.nl/Content/View.aspx?piid=13894) describes devices properties and behavior. Several implementations will be available. Universidad de Zaragoza Java Interfaces Reference Implementation and osgi bundle Platforms: Windows, Mac, Linux

A SOA-based framework for multilingual question answering (QA) systems that answer natural language questions with the help of a domain ontology and structured answer data sources from freely specifiable domains. Platforms: Windows, Mac, Linux

Tools designed to assist in creating and using the RadLex ontology (http://www.radlex.org). Platforms: Windows, Mac, Linux

Semtinel is an application framework for the semi-automatic creation, maintenance and analysis of hierarchical concept schemes (thesaurus, classification or ontology). Semtinel supports the development of new analysis methods and visualization techniques Platforms: Windows, Mac, Linux

A simple tool for sketching out ontology structures, including OWL export. Developed at the University of Manchester as a third-year project. Platforms: Windows, Mac, Linux

WSMO Studio is a Semantic Web Service and Semantic Business Process modelling environment based on the Web Services Modelling Ontology (WSMO). WSMO Studio is available as a set of Eclipse plug-ins that can be extended and customised by 3rd parties. Platforms: Windows, Mac, Linux

The SMW OntologyEditor is an extension of SemanticMediaWiki and has been developed as part of the ACTIVE project in order to enable the development of lightweight ontologies and to provide knowledge repair algorithms. Platforms: PHP

OntoCreator is a tool able to automatically create synthetic ontologies according to user given adjustable specifications with respect to size, distribution of certain language construct and expressivity. The current version will generate ontologies according to the ?*a*ffnet einen externen Link... Platforms: Mac

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac

Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats. SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv",... Platforms: *nix

Vector Visuals provides an easy-to-use, object-based API for creating and manipulating Java2D-rendered shapes and images. The project features object embedding, dynamic connectors, and multithreaded task support. Vector Visuals has been downloaded thousands of times, and is already in use in a... Platforms: *nix

Platypus Wiki provides a semantic Wiki Wiki Web. Platypus Wiki is an enhanced Wiki Wiki Web with ideas taken from Semantic Web. It offers a simple user interface for creating Wiki page plus metadata according to W3C standards. Weve chosen HTMLarea v3.0rc1 as a WYSIWYG editor for creating... Platforms: *nix

GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford... Platforms: *nix