Synthetic Biology:Semantic web ontology/Software

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RDF

• Developers Guide to Semantic Web Toolkits for different Programming Languages
• Scalability Report on Triple Store Applications
• Jena - a Java framework for building Semantic Web applications. It provides a programmatic environment for RDF, RDFS and OWL, including a rule-based inference engine.
  • jena-dev - Jena developers mailing list archive
  • Jena relational database backend
    • How to create persistent models
    • Persistent ontologies example
    • Jena2 MySQL howto
  • Joseki - a SPARQL Server for Jena
  • ARQ - a SPARQL Processor for Jena
  • Eyeball: checking RDF/OWL for common problems
  • Jena2 Manager
• 4Suite™: an open-source platform for XML and RDF processing
• Sesame: an open source RDF database with support for RDF Schema inferencing and querying
• kowari|metastore: database for the storage, retrieval and analysis of RDF and OWL metadata
• ARC RDF Store is a SPARQL-enabled RDF storage system optimized for shared, hosted (or otherwise performance-limited) Web environments.
• Redland RDF Application Framework (Redland RPMs)
• 3store - developed in the Intelligence, Agents and Multimedia research group at Southampton University, as part of the AKT Project.
• RDF Validator
• Wilbur Nokia RDF toolkit
• ARP: Another RDF Parser (Jena RDF/XML Parser, from Jeremy Carroll @ HP)
• Oracle Semantic Technologies - links to the white papers at the bottom of the page
  • RDF data model in Oracle - white paper decribing DB schema for RDF statements storage
• MySQL Dmoz RDF Parser - This Perl script converts the Dmoz content.rdf file from the RDF format into a text file which can be easily loaded into MySQL.
• ActiveRDF is a library for accessing RDF data from Ruby programs.
• RDFRoom is an isometric RDF viewer. It gives the user ways to view and manipulate his RDF data that might make him see the data in a brand new perspective.

RDF Schema

• RDF Schema formatter - extracts human readable information from a RDF Schema

Ontology editors

• List of ontology editors
• Ontology tools survey @ xml.com from 2004
• Protégé is a free, open source ontology editor and knowledge-base framework
  • Protégé OWL Plugin - ontology editor for the Semantic Web
  • Projects that use Protégé
  • OWL-S Editor is a Tab Widget plugin for Protégé
• OilEd is an ontology editor allowing the user to build ontologies using DAML+OIL
• Ontolingua
• Chimaera is a software system that supports users in creating and maintaining distributed ontologies on the web
• SWOOP A Hypermedia-based Featherweight OWL Ontology Editor
• Altova SemanticWorks - visual RDF and OWL editor that autogenerates RDF/XML and N-Triples
• CmapTools Ontology Editor - concept maps provide a human-centered interface to display the structure, content, and scope of an ontology
• SweDE is built on the Eclipse IDE, includes an OWL editor with helpful features like syntax highlighting, autocompletion, and error-detection. It also currently integrates existing tools like the OWL Validator, Kazuki (OWL to Java code generator), and DumpOnt (Ontology Visualizer).
• m3t4.studio Semantic Toolkit - RDF and OWL editors for the Eclipse IDE.

Query

• SPARQL engine
• sparql2sql - a query engine for SPARQL over Jena triple stores
• Javascript SPARQL library and AJAX SPARQL client
• Tabulator: AJAX and Semantic Web - browser
• RDF Query-o-matic Light
• SPARQLer - an RDF Query server

Rule engines

• CWM - Closed World Machine
• Pychinko: Rete-based RDF friendly rule engine

Companies

• Oracle Semantic Technologies Center
• Semantic Web Research at HP Labs

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