Ontology

FastSemSim is specially designed as a handy Python-based efficient implementation of a couple of semantic similarity measures. The main target of the project is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology Platforms: Windows

MEFIT, also known as the Microarray Experiment Functional Integration Technology is developed as a system for microarray integration. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions.... Platforms: Windows

Key Concepts Extraction was specially developed in order to help you perform key-concept extractions from ontologies. In order to use the KCE API you have to import the available JAR packages into your project. The packages you have to import are: · kce.jar · taxonomy.jar ·... Platforms: Windows

jMapper was specially designed as an accessible component created using the Java programming language. It was built in order to allow you to automatically detect metaphors / analogies between two domains (ontologies). Platforms: Windows

Apolda, also known as Automated Processing of Ontologies with Lexical Denotations for Annotation was built as a plugin for GATE. The Apolda processing resource (PR) annotates a document like a gazetteer, but takes the terms from an (OWL) ontology rather than from a list. Apolda searches the... Platforms: Windows

CRML - Conflict Resolution Markup Language - http://www.equiforum.org - is an open source innitiative to develop an XML based Semantic Web ontology (RDF, OWL) for researchers interested in peace to create a standard way of collecting and sharing informa Platforms: Windows, Mac, Linux

The EURP OntoLookup is a CREOLE plugin for GATE http://www.gate.ac.uk/ which uses an OWL ontology for lookup. It has a very fast implementation based on a tree of hash maps. Platforms: Windows, Mac, Linux

The JMX Extension package provides the capability to manage selective Protg OWL API remotely using the JMX library. This package allows distributed software components to retrieve, contribute, and reason about information in single OWL ontology. Platforms: Windows, Mac, Linux

Mimosa is a modeling and simulation platform, covering the process from building conceptual models to running the simulations. The specification uses ontologies and an extensible set of formalisms for the dynamics. The simulation kernel is based on DEVS. Features: * Ontology editor for... Platforms: Mac

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java. Platforms: Windows, Mac, Linux

OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework. Platforms: Windows, Mac, Linux

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID. Platforms: Windows, Mac, Solaris, Linux

PDKB is an Artificial Intelligence Knowledge Bank of commonsense rules and facts. It is based on the Cyc Upper Ontology and the MELD language. Platforms: Windows, Mac, Linux

S-Match is a semantic matching framework. S-Match takes any two tree like structures (such as database schemas, classifications, lightweight ontologies) and returns a set of correspondences between those tree nodes which semantically correspond to one another. S-Match contains implementations... Platforms: Windows, Mac, Linux

The VilAug framework for visual linguistics! This gadget contains an IconNet with icons like WordNet and an IconMessenger as instant messenger. A new ontology is used, grammars for visual languages designed. A language with signs? Create it with VilAug. Platforms: Windows, Mac, Linux

Blast2GO?*A* is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features are: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are... Platforms: Mac

Ontopia is a set of tools which contains everything you need to build a full Topic Maps-based application. Using Ontopia you can design your ontology, populate the topic map manually and/or automatically, build the user interface, show graphical visualizations of the topic map, and much more.... Platforms: Mac

OntoUML Editor is a model-based graphical editor that supports the creation of conceptual models and domain ontologies in a philosophically and cognitively well-founded modeling language named OntoUML, which is based on the Unified Foundational Ontology (UFO). The editor is designed in a way... Platforms: Mac

PRIDE Converter converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS). The... Platforms: Mac

Knowtator is a general-purpose text annotation tool that is integrated with the Prot?*A*g?*A* knowledge representation system. Knowtator facilitates the manual creation of training and evaluation corpora for a variety of biomedical language processing tasks. Building on the strengths of the... Platforms: Mac