Synthetic Biology:Semantic web ontology/Software

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• Semantic Web Tools from ESW wiki
• SIMILE is focused on developing robust, open source tools based on Semantic Web technologies that improve access, management and reuse among digital assets

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
• SemWebCentral - open source tools for the Semantic Web
• RDF in Mozilla: RDF engine, code examples, etc
• RDF module of JSLib

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.
• 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

Servers

"semantic repository"

reasoner, ontology server, semantic store, metastore, RDF database (reference)

• 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
  • Introduction to Jena from IBM
  • Jena Javadoc
  • Jena relational database backend
    • How to create persistent models
    • Persistent ontologies example
    • Jena2 MySQL howto
  • Joseki is an HTTP and SOAP engine supports the SPARQL Protocol and the SPARQL RDF Query language
  • ARQ is a query engine for Jena that supports the SPARQL RDF Query language
  • LARQ - Lucene + ARQ
  • 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
  • OWLIM - OWL Semantic Repository packaged as a Storage and Inference Layer (SAIL) for the Sesame RDF database
• Kowari: database for the storage, retrieval and analysis of RDF and OWL metadata; non-relational, written in Java.
• Mulgara is a scalable RDF database written entirely in Java. Mulgara is an Open Source fork of Kowari.
• ARC - RDF and SPARQL for PHP developers is a lightweight, SPARQL-enabled RDF system for mainstream Web projects. It is written in PHP and has been optimized for shared (or otherwise performance- or privilege-limited) Web environments.
• 3store - a C library that uses MySQL to store its raw RDF data and caches, part of the AKT Project.
• OpenDFKI RDFBroker is an RDF store that uses a natural mapping of RDF resources to database tables that does not rely on RDF Schema, but constructs a schema based on the occurring signatures, where a signature is the set of properties used on a resource
• 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
• Nokia Semantic Web Server - reference implementation of URIQA (URI Query Agent) model. Provides access to metadata describing products, documents, vocabularies, schemas, and other resources.
  • Sourceforge page. For MS Windows only.
  • Tools & Utilities
• SMART: System for Managing Applications based on RDF Technology

Commercial

• Intellidimension 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
• AllegroGraph
  • scalable RDF triple store with advanced query and reasoning capabilities
  • free Java version works with up to 50 million triples

Life Sciences

• myGrid is a collection of services and components that allows the high level integration of biological data and applications.
  • Feta - a semantic discovery tool to search available web services
  • LSID components - LSIDs are used as unique identifiers for data objects that are imported or created in myGrid. This facilitates data retrieval, data searching and provenance capture
  • BioServices - provide mechanisms for producing web services from exisiting bioinformatics services for use in workflows
• myExperiment is a collaborative platform for life scientists to manage, share and find Taverna workflows
• Smart Tea is about improving the information environment for chemists doing chemistry - within and beyond the lab
• myTea - extending Smart Tea Interaction to myGrid BioInformatics
  • myTea vLab - software environment for bioinformatics
• Semantic Grid is an extension of the current Grid in which information and services are given well-defined meaning through machine-processable descriptions
• Wiki for Professionals are workspace for Semantic Web, enabling real-time knowledge exchange and exploration
  • developed by Knewco, Inc

Toolkits

• Developers Guide to Semantic Web Toolkits for different Programming Languages
• Redland RDF Application Framework: modular, object based libraries written in C (Redland RPMs)
  • RDF-Redland - a Ruby Wrapper around the Redland Application Framework
  • Storage modules
• 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.
• JRDF - Java RDF API
• TAP @ Stanford
• The Protégé OWL API
• Perl
  • Perllib - the W3C Perl Code Library
  • CARA Perl RDF API - a pure perl RDF system providing storage and RDF/XML parsing
  • Perl RDF API
• PHP
  • RAP - is a software package for parsing, searching, manipulating, serializing and serving RDF models.
  • pOWL - Semantic Web Development Platform - web-based ontology edititing and management solution
  • ARC - easy RDF and SPARQL for LAMP systems
• Python
  • RDFLib - Python library for working with RDF (RDFLib Wiki)
  • Oort - a Python toolkit for accessing RDF graphs as plain objects (it has RDFLib under the crust)
  • 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
• 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 (another link)
  • SWCLOS: A Semantic Web Processor on Common Lisp Object System
• Adobe's Extensible Metadata Platform (XMP) is a labeling technology that allows you to embed data about a file, known as metadata, into the file itself.
• Crow: Computational Representation Of Whatever is a java library for the manipulation and mining of complex and world-wide distributed data (by Raik Grünberg)
  • Sourceforge project page
• Semantic Web programming languages
  • Adenine is a python like language that knows how to deal with RDF. It is used to implement Haystack.
  • Fabl
• org.biojava.ontology: a general-purpose API for ontologies

Browsers

• Tabulator: AJAX and Semantic Web - browser
  • Slicing and dicing web data with Tabulator
• SIMILE Longwell is a web-based RDF browser
• SIMILE Welkin - visualizes RDF models
• BrownSauce generic RDF browser
• foafnaut - SVG FOAF browser
• FoaF Explorer
• Haystack
  • What is Haystack?
  • Info for developers - useful links
  • Haystack: A Platform for Authoring End User Semantic Web Applications
• OINK: Open Integration of Networked Knowledge (by Ora Lassila, based on Wilbur)
• AKT Triplestore Browser
• OpenLink Data Explorer Extension for Firefox allows Web users to explore the raw data and data relationships that underly a Web page
• jOWL is a jQuery plugin for navigating and visualising OWL-RDFS documents.

Editors

• morla is a multiplatform editor of RDF documents
• IsaViz: A Visual Authoring Tool for RDF
• RDF Backend for Protégé - create, import, and save RDF(S) files in in Protégé
• Fentwine: A navigational RDF browser and editor
• Simplistic RDF Editor - needs SVG
• RDF Editor in Java - simple
• RDFAuthor is a tool designed to ease the pain of creating RDF instance data. Authoring is largely a matter of dragging in data and binding it together using a graphical interface.
• Eclipse-based
  • RDFX is a suite of plug-ins for the Eclipse platform which together provide a framework for experimentation with RDF
• Web-based
  • Leeet prototype demo - search with auto-complete, etc

IDEs

TopBraid Composer

• commercial development environment for W3C's Semantic Web standards RDF Schema, the OWL Web Ontology Language, the SPARQL Query Language and the Semantic Web Rule Language (SWRL)
• provides scalable database backends (Jena, AllegroGraph, Oracle 10g and Sesame) as well as multi-user support

Parsers

• Simple javascript RDF parser
• 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

• Visualizing RDF - list of tools that allow viewing RDF document as a diagram
• 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.
  • Styling RDF Graphs with GSS - Graph Stylesheets
• 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).
• OWLDoc is a tool that generates JavaDoc style html page documentation for an OWL ontology.
• Gadget is an XML inspector. It is able to process large quantities of well-formed XML and produce a condensed summary of that data. Live demo
• RDF-Gravity is a tool for visualising RDF/OWL Graphs/ontologies (Java Web Start)

Other

• Ontoware - Semantic Web related software projects
• RDF Validator

• RDB to RDF
  • W3C Workshop on RDF Access to Relational Databases
  • D2R Map - Database to RDF Mapping Language and Processor
  • D2RQ - Treating Non-RDF Databases as Virtual RDF Graphs
    • D2RQ User Manual and Language Specification
    • D2R MAP - a database to RDF mapping language (poster from WWW2003)
    • D2RQ — Lessons Learned: position paper for the W3C Workshop on RDF Access to Relational Databases
  • 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 database content to ontologies.
  • Triplify is a small plugin for Web applications, which reveals the semantic structures encoded in relational databases by making database content available as RDF, JSON or Linked Data.

• 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
• Pike is a dynamic programming language for the semantic web with a syntax similar to Java and C (examples of Semantic Web support)

Benchmarks

Lehigh University Benchmark (LUBM) is developed to facilitate the evaluation of Semantic Web repositories in a standard and systematic way

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 (COE) - concept maps provide a human-centered interface to display the structure, content, and scope of an ontology
  • CmapTools knowledge modeling kit from the Institute of Human and Machine Cognition (IHMC)
  • CmapTools project description
• 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.
  • m3t4 wiki
• SMORE - Create OWL Markup for HTML Web Pages
• OntoMat-Annotizer is a user-friendly interactive webpage annotation tool.
• Hozo - from Osaka University, Java-based
• 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 - allows to graphically create and edit RDF instance documents, RDFS vocabularies, and OWL ontologies with full syntax checking

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
• LexGrid - an infrastructure for interlocking biomedical concepts across vocabularies and ontologies
• IBM Web Ontology Manager

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

• BaseVISor is VIStology's versatile forward-chaining inference engine specialized to handle facts in the form of RDF triples with support for RuleML, R-Entailment and XML Schema Datatypes.
• 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
• Inference_engine
• 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
• SIE - Simple Inference Engine written in Ruby
• JBoss Rules - an open source and standards-based business rules engine
• SMILE (Structural Modeling, Inference, and Learning Engine) is a fully portable library of C++ classes implementing graphical decision-theoretic methods

Commercial

RacerPro (Renamed ABox and Concept Expression Reasoner) is an OWL reasoner and inference server (also available from Franz Inc)

Web Services

• The Universal Information Service Browser (UISB) Project The aim of the UISB Project is to investigate and improve interaction with Information Services used in a range of distributed environments, in the first instance these will include Web Services, UDDI and the Jini Lookup Service.

Live demos

• Lee Feigenbaum: semantic web demos
• Redland Rasqal RDF Query Demo
• Redland Raptor RDF Parser Demo

Companies

• Oracle Semantic Technologies Center
• Semantic Web Research at HP Labs
• IBM alphaWorks : Semantics
• Nokia Semantic Web - Research Program
  • SwapMe (Semantic Web Application Platform for Mobile Ecosystems) project will develop a new software architecture that will enable the mobile ecosystem to take maximum advantage of the power of the Semantic Web data model
• Teranode XDA
• Radar Networks
• Metaweb Technologies
• Powerset - natural language search
• Franz Inc develops AllegroGraph triple-store which works with RacerPro reasoner and TopBraid Composer Semantic Web IDE
• Cambridge Semantics - middleware platforms (people)

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