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

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*[http://rdfreactor.ontoware.org/ RDFReactor] views the RDF data model through object-oriented Java proxies.
*[http://rdfreactor.ontoware.org/ RDFReactor] views the RDF data model through object-oriented Java proxies.
*[http://tap.stanford.edu/ TAP] @ Stanford
*[http://tap.stanford.edu/ TAP] @ Stanford
*[http://www.wiwiss.fu-berlin.de/suhl/bizer/rdfapi/ RAP] - RDF API for PHP
*[http://protege.stanford.edu/plugins/owl/api/ The Protégé OWL API]
*[http://protege.stanford.edu/plugins/owl/api/ The Protégé OWL API]
*PHP
**[http://www.wiwiss.fu-berlin.de/suhl/bizer/rdfapi/ RAP] - RDF API for PHP
**[http://powl.sourceforge.net/ pOWL] - Semantic Web Development Platform - web-based ontology edititing and management solution


===Browsers===
===Browsers===

Revision as of 16:08, 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.
  • Brahms - RDF/S Main Memory Storage

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 On Rails and ActiveRDF - HCLSIG subgroup task - to produce a Ruby On Rails and Active RDF implementation of the BioDash eclipse (Java) based gui so that we can show that the functionality shown in BioDash can be implemented using web based technologies.
  • 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
  • The Protégé OWL API
  • PHP
    • RAP - RDF API for PHP
    • pOWL - Semantic Web Development Platform - web-based ontology edititing and management solution

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
  • BioDash is a Semantic Web prototype of a Drug Development Dashboard that associates disease, compounds, drug progression stages, molecular biology, and pathway knowledge for a team of users (built on Haystack)

RDF Schema

Ontology editors

Query

Rule engines

  • A reasoner is a service that takes the statements encoded (asserted) in an ontology as input and derives (infers) new statements from them. In particular, OWL reasoners can be used to:
    • Reveal subclass/superclass relationships among classes
    • Determine the most specific types of individuals
    • Detect inconsistent class definitions
  • CWM - Closed World Machine
  • Pychinko: Rete-based RDF friendly rule engine
  • Pellet is an open-source Java based OWL DL reasoner. It can be used in conjunction with both Jena and OWL API libraries and also provides a DIG interface.

Companies

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