Synthetic Biology:Semantic web ontology/Software

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RDF

• Developers Guide to Semantic Web Toolkits for different Programming Languages
• Scalability Report on Triple Store Applications
• Oracle Semantic Technologies - links to the white papers at the bottom of the page
• Intellidimension Labs - A Collection of RDF Gateway Demos, Examples, and Experiments (Uniprot, etc)

RDF and other formats

• RDF data model in Oracle - white paper (PDF) decribing DB schema for RDF statements storage.
• Storing RDF in a relational database
• Relational Databases on the Semantic Web from Design Issues.
• Mapping Semantic Web Data with RDBMSes from SWAD Europe.
• Databases, Query, API, Interfaces report on Query languages from SWAD Europe.
• D2R Map poster from WWW2003
• Protégé JDBC backend design rationale
• RDF access to relational databases
• Nuts and bolts from HCLSIG BioRDF - tools for converting data in various formats to RDF
• Bridging the Gap between RDF and XML
• 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.
  • Demonstration of GRDDL applied to XML
  • Bridging XHTML, XML and RDF with GRDDL
  • GRDDL Data Views - a way of extracting Semantic Web data in RDF from XML formats (especially XHTML dialects or microformats) via transformations identified by URIs and typically expressed in XSLT

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.
  • jena-dev - Jena developers mailing list archive
  • An Introduction to RDF and the Jena RDF API
  • Jena Javadoc
  • Jena relational database backend
    • How to create persistent models
    • Persistent ontologies example
    • Jena2 MySQL howto
  • Joseki - a SPARQL Server for Jena
  • ARQ - a SPARQL Processor for Jena
  • Eyeball: checking RDF/OWL for common problems
  • Jena2 Manager
• 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.
  • Virtuoso OpenSource Edition

Libraries

• Wilbur Nokia RDF toolkit written in Common LISP
• Redland RDF Application Framework (Redland RPMs)
  • RDF-Redland - a Ruby Wrapper around the Redland Application Framework
  • Redland Rasqal RDF Query Demo
  • Redland Raptor RDF Parser Demo
• 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
  • RDFLib Wiki
• 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

• Tabulator: AJAX and Semantic Web - browser
• SIMILE Longwell is a web-based RDF browser
• SIMILE Welkin - visualizes RDF models
• BrownSauce generic RDF browser
• foafnaut - SVG FOAF browser
• Haystack
  • What is Haystack?
• IsaViz: A Visual Authoring Tool for RDF
• Fentwine: A navigational RDF browser and editor
• Simplistic RDF Editor - needs SVG
• RDF Editor in Java - simple

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

• RDF Schema formatter - online tool that 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
  • Projects that use Protégé
  • OWL-S Editor is a Tab Widget plugin for Protégé
• 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.
• IBM Integrated Ontology Development Toolkit

Query

• SPARQL engine
• sparql2sql - a query engine for SPARQL over Jena triple stores
• Javascript SPARQL library and AJAX SPARQL client
• RDF Query-o-matic Light
• SPARQLer - an RDF Query server

Rule engines

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

Companies

• Oracle Semantic Technologies Center
• Semantic Web Research at HP Labs

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