Synthetic Biology:Semantic web ontology/Software

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*[http://www.raiks.de/crow/ Crow]: Computational Representation Of Whatever is a java library for the manipulation and mining of complex and world-wide distributed data (by [[User:Raik|Raik Grünberg]])
*[http://www.raiks.de/crow/ Crow]: Computational Representation Of Whatever is a java library for the manipulation and mining of complex and world-wide distributed data (by [[User:Raik|Raik Grünberg]])
**[http://crow.sourceforge.net/ Sourceforge project page]
**[http://crow.sourceforge.net/ Sourceforge project page]
 +
*[http://haystack.csail.mit.edu/developers/adenine.html Adenine] is a python like language that knows how to deal with RDF.  It is used to implement [http://haystack.lcs.mit.edu/ Haystack].
===Browsers===
===Browsers===

Revision as of 19:45, 29 August 2006

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RDF

RDF and other formats

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.
  • 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.
  • 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
  • Nokia Semantic Web Server - reference implementation of URIQA (URI Query Agent) model. Provides access to metadata describing products, documents, vocabularies, schemas, and other resources.
  • 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
  • SMART: System for Managing Applications based on RDF Technology

Commercial

Toolkits

  • Redland RDF Application Framework: modular, object based libraries written in C (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.
  • Pyrple - Python 2.3 RDF toolkit
  • JRDF - Java RDF API
  • TAP @ Stanford
  • The Protégé OWL 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
  • 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)
  • Adenine is a python like language that knows how to deal with RDF. It is used to implement Haystack.

Browsers

Editors

Parsers

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.
  • 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

Other

  • Ontoware - Semantic Web related software projects
  • 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
  • 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

Ontology editors

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

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

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.

Companies

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