Synthetic Biology:Semantic web ontology/Software

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RDF

RDB-RDF

Triple Stores

Commercial

  • RDF Gateway - commercial Windows app but free version available
  • Virtuoso is an innovative Virtualization platform that transparently integrates Data, Services, and Business Processes across the enterprise.

Libraries

Browsers

Parsers

  • ARP: Another RDF Parser (Jena RDF/XML Parser, from Jeremy Carroll @ HP)
  • 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.

Visualization

  • 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.
  • IsaViz is a visual environment for browsing and authoring RDF models represented as graphs.

Other

  • RDF Validator
  • D2R Map - Database to RDF Mapping Language and Processor
  • RDFizers are tools that allow to transform existing data into an RDF representation.

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
  • 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

Rule engines

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

Companies

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