Synthetic Biology:Semantic web ontology/Software: Difference between revisions

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*[http://labs.intellidimension.com/demo/default.rsp Intellidimension Labs] - A Collection of RDF Gateway Demos, Examples, and Experiments (Uniprot, etc)
*[http://labs.intellidimension.com/demo/default.rsp Intellidimension Labs] - A Collection of RDF Gateway Demos, Examples, and Experiments (Uniprot, etc)


===RDB-RDF===
===RDF and other formats===
*[http://download.oracle.com/otndocs/tech/semantic_web/pdf/w3d_rdf_data_model.pdf RDF data model in Oracle] - white paper (PDF) decribing DB schema for RDF statements storage.
*[http://download.oracle.com/otndocs/tech/semantic_web/pdf/w3d_rdf_data_model.pdf RDF data model in Oracle] - white paper (PDF) decribing DB schema for RDF statements storage.
*[http://www-db.stanford.edu/~melnik/rdf/db.html Storing RDF in a relational database]
*[http://www-db.stanford.edu/~melnik/rdf/db.html Storing RDF in a relational database]
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*[http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Nuts_and_bolts Nuts and bolts from HCLSIG BioRDF] - tools for converting data in various formats to RDF
*[http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Nuts_and_bolts Nuts and bolts from HCLSIG BioRDF] - tools for converting data in various formats to RDF
*[http://www-db.stanford.edu/~melnik/rdf/fusion.html Bridging the Gap between RDF and XML]
*[http://www-db.stanford.edu/~melnik/rdf/fusion.html Bridging the Gap between RDF and XML]
*[http://www.w3.org/TR/grddl/ GRDDL] - Gleaning Resource Descriptions from Dialects of Languages.  A mechanism for getting RDF data out of XML and XHTML documents using explicitly associated transformation algorithms, typically represented in XSLT.


===Triple Stores===
===Triple Stores===

Revision as of 11:29, 8 May 2006

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RDF

RDF and other formats

Triple Stores

  • 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.
  • 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: database for the storage, retrieval and analysis of RDF and OWL metadata; non-relational, written in Java.
  • ARC RDF Store is a SPARQL-enabled RDF storage system optimized for shared, hosted (or otherwise performance-limited) Web environments.
  • 3store - developed in the Intelligence, Agents and Multimedia research group at Southampton University, as part of the AKT Project.
  • rdfDB: An RDF Database
  • RDFStore - Perl/C RDF storage and API
  • KAON is an open-source ontology management infrastructure targeted for business applications. It includes a comprehensive tool suite allowing easy ontology creation and management and provides a framework for building ontology-based applications. An important focus of KAON is scalable and efficient reasoning with ontologies.
  • ParkaSW is an inferencing database, built for use with the semantic web. It is currently undergoing revision to support RDF internally.

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

  • Wilbur Nokia RDF toolkit written in Common LISP
  • Redland RDF Application Framework (Redland RPMs)
  • ActiveRDF is a library for accessing RDF data from Ruby programs.
  • Ruby RDF was an experimental RDF system implemented in Ruby. It is no longer under active development.
  • RDFLib - Python library for working with RDF
  • Sparta is an Python API for RDF that is designed to help easily learn and navigate the Semantic Web programmatically. Unlike other RDF interfaces, which are generally triple-based, Sparta binds RDF nodes to Python objects and RDF arcs to attributes of those Python objects.
  • JRDF - Java RDF API
  • RDFReactor views the RDF data model through object-oriented Java proxies.
  • TAP @ Stanford
  • RAP - RDF API for PHP

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
  • D2RQ - Treating Non-RDF Databases as Virtual RDF Graphs
  • KAON Reverse is a prototype GUI for mapping relational databse content to ontologies.
  • RDFizers are tools that allow to transform existing data into an RDF representation.
  • Tripletest is a testing framework for RDF triplestores

RDF Schema

Ontology editors

Query

Rule engines

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

Companies

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