Synthetic Biology:Semantic web ontology/Software

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RDF

• RDF Validator
• 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
• Redland RDF Application Framework (Redland RPMs)
• 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

RDF Schema

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

Ontology editors

• Protégé is a free, open source ontology editor and knowledge-base framework
• Protégé OWL Plugin - ontology editor for the Semantic Web
• 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

Query

• SPARQL engine

Rule engines

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

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