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
• 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

• 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 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
  • 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.
• Pyrple - Python 2.3 RDF toolkit
• JRDF - Java RDF API
• TAP @ Stanford
• The Protégé OWL API
• PHP
  • RAP - RDF API for PHP
  • pOWL - Semantic Web Development Platform - web-based ontology edititing and management solution
• Java code generators
  • RDFReactor views the RDF data model through object-oriented Java proxies; Java interfaces are generated automatically from an RDF Schema
  • Kazuki generates a Java API for working with OWL instance data directly from a set of OWL ontologies. It is built on Jena 2 and mirrors their ontology interface.
  • Jastor is a open source Java code generator that emits Java Beans from Web Ontologies (OWL) enabling convenient, type safe access and eventing of RDF stored in a Jena Semantic Web Framework model.
• LISP
  • Wilbur Nokia RDF toolkit written in Common LISP
  • SWCLOS: A Semantic Web Processor on Common Lisp Object System

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
• Eclipse-based
  • RDFX is a suite of plug-ins for the Eclipse platform which together provide a framework for experimentation with RDF

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.
• Rudolf: online RDF Visualizer
• DumpOnt is a program to display the class and property hierarchies present in an RDF Schema or DAML+OIL or OWL ontology (based on Jena2).

Other

• RDF Validator
• RDB to RDF
  • D2R Map - Database to RDF Mapping Language and Processor
  • D2RQ - Treating Non-RDF Databases as Virtual RDF Graphs
  • D2R Server - SPARQL endpoint for relational databases; combines the D2RQ API and Joseki SPARQL Server to map a database's contents into a virtual RDF graph that can be accessed over the SPARQL protocol. It is bundled with a Jetty webserver and aims at being easy to set up and use.
  • 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 crawlers
  • RDF crawler - uses Jena RDF toolkit to spider the web gathering up semantic web data and to store it in any of Jena's backend stores
  • OntoBroker - Java-based

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
• SWOOP A Hypermedia-based Featherweight OWL Ontology Editor
• 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.
• SMORE - Create OWL Markup for HTML Web Pages
• OntoMat-Annotizer is a user-friendly interactive webpage annotation tool.
• Commercial
  • IBM Integrated Ontology Development Toolkit - IODT
    • EODM Workbench is part of IODT
  • OntoStudio is the leading engineering environment for ontologies and for the development of semantic applications; based on Eclipse
  • Altova SemanticWorks - visual RDF and OWL editor that autogenerates RDF/XML and N-Triples

Ontology Managers

• 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.
• KAON2 is an infrastructure for managing OWL-DL and SWRL ontologies.
• Chimaera is a software system that supports users in creating and maintaining distributed ontologies on the web

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

• 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
• DIG interface provides uniform access to Description Logic (DL) Reasoners (DIG interface on SourceForge)
  • a number of reasoners including FaCT++, RACER, and Pellet provide support for DIG
  • a number of ontology editors (including OilEd, Protege and SWOOP) can use the DIG interface to communicate with such reasoners
  • Jena framework also makes use of DIG for reasoning over OWL ontologies
• 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.
• FaCT++ is the new generation of the well-known FaCT OWL-DL reasoner
• Commercial
  • RacerPro is an OWL reasoner and inference server

Companies

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

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