Synthetic Biology:Semantic web ontology/Software
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RDF
- 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
- Jena2 Manager
- 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
- 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.
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
- 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).
Query
Rule engines
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