Synthetic Biology:Semantic web ontology/Software - Revision history

Ilya: /* Browsers */

2009-01-12T21:25:23Z

Browsers

←Older revision		Revision as of 21:25, 12 January 2009
Line 137:		Line 137:
	*[http://triplestore.aktors.org/browse/ AKT Triplestore Browser]		*[http://triplestore.aktors.org/browse/ AKT Triplestore Browser]
	*[http://ode.openlinksw.com/ OpenLink Data Explorer Extension] for Firefox allows Web users to explore the raw data and data relationships that underly a Web page		*[http://ode.openlinksw.com/ OpenLink Data Explorer Extension] for Firefox allows Web users to explore the raw data and data relationships that underly a Web page
		+	*[http://jowl.ontologyonline.org/ jOWL] is a jQuery plugin for navigating and visualising OWL-RDFS documents.

	====Editors====		====Editors====

Ilya: /* Rule engines */

2008-09-09T22:26:05Z

Rule engines

←Older revision		Revision as of 22:26, 9 September 2008
Line 241:		Line 241:

	==Rule engines==		==Rule engines==
		+	*[http://www.vistology.com/basevisor/ 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:		*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		**Reveal subclass/superclass relationships among classes

Ilya: /* Browsers */

2008-08-13T04:05:06Z

Browsers

←Older revision		Revision as of 04:05, 13 August 2008
Line 136:		Line 136:
	*[http://wiki.nrcc.noklab.com/SwapMe/OINK OINK]: Open Integration of Networked Knowledge (by Ora Lassila, based on Wilbur)		*[http://wiki.nrcc.noklab.com/SwapMe/OINK OINK]: Open Integration of Networked Knowledge (by Ora Lassila, based on Wilbur)
	*[http://triplestore.aktors.org/browse/ AKT Triplestore Browser]		*[http://triplestore.aktors.org/browse/ AKT Triplestore Browser]
		+	*[http://ode.openlinksw.com/ OpenLink Data Explorer Extension] for Firefox allows Web users to explore the raw data and data relationships that underly a Web page

	====Editors====		====Editors====

Ilya: /* Editors */

2008-06-23T21:25:41Z

Editors

←Older revision		Revision as of 21:25, 23 June 2008
Line 147:		Line 147:
	*Eclipse-based		*Eclipse-based
	**[http://www.rdfx.org/ RDFX] is a suite of plug-ins for the Eclipse platform which together provide a framework for experimentation with RDF		**[http://www.rdfx.org/ RDFX] is a suite of plug-ins for the Eclipse platform which together provide a framework for experimentation with RDF
		+	*Web-based
		+	**[http://neuroscientific.net/leeet/ Leeet prototype demo] - search with auto-complete, etc

	====IDEs====		====IDEs====

Ilya: /* Other */

2008-06-09T21:20:55Z

Other

←Older revision		Revision as of 21:20, 9 June 2008
Line 172:		Line 172:
	*[http://www.ontoware.org/ Ontoware] - Semantic Web related software projects		*[http://www.ontoware.org/ Ontoware] - Semantic Web related software projects
	*[http://www.w3.org/RDF/Validator RDF Validator]		*[http://www.w3.org/RDF/Validator RDF Validator]
		+
	*RDB to RDF		*RDB to RDF
	**[http://www.w3.org/2007/03/RdfRDB/ W3C Workshop on RDF Access to Relational Databases]		**[http://www.w3.org/2007/03/RdfRDB/ W3C Workshop on RDF Access to Relational Databases]
Line 181:		Line 182:
	**[http://www.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/ 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.		**[http://www.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/ 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.
	**[http://kaon.semanticweb.org/alphaworld/reverse KAON Reverse] is a prototype GUI for mapping relational database content to ontologies.		**[http://kaon.semanticweb.org/alphaworld/reverse KAON Reverse] is a prototype GUI for mapping relational database content to ontologies.
		+	**[http://triplify.org/Overview 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.
		+
	*[http://simile.mit.edu/RDFizers/ RDFizers] are tools that allow to transform existing data into an RDF representation.		*[http://simile.mit.edu/RDFizers/ RDFizers] are tools that allow to transform existing data into an RDF representation.
	*[http://tripletest.sourceforge.net/ Tripletest] is a testing framework for RDF triplestores		*[http://tripletest.sourceforge.net/ Tripletest] is a testing framework for RDF triplestores

Ilya: /* Toolkits */

2008-03-07T00:09:43Z

Toolkits

←Older revision		Revision as of 00:09, 7 March 2008
Line 91:		Line 91:
	**[http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Ruby_On_Rails_and_ActiveRDF 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.		**[http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Ruby_On_Rails_and_ActiveRDF 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.
	*[http://www.w3.org/2001/12/rubyrdf/intro.html Ruby RDF] was an experimental RDF system implemented in Ruby. It is no longer under active development.		*[http://www.w3.org/2001/12/rubyrdf/intro.html Ruby RDF] was an experimental RDF system implemented in Ruby. It is no longer under active development.
-	*[http://rdflib.net/ RDFLib] - Python library for working with RDF
-	**[http://wiki.python.org/moin/RdfLib RDFLib Wiki]
-	*[http://www.mnot.net/sw/sparta/ 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.
-	*[http://infomesh.net/pyrple/ Pyrple] - Python 2.3 RDF toolkit
	*[http://jrdf.sourceforge.net/ JRDF] - Java RDF API		*[http://jrdf.sourceforge.net/ JRDF] - Java RDF API
	*[http://tap.stanford.edu/ TAP] @ Stanford		*[http://tap.stanford.edu/ TAP] @ Stanford
Line 105:		Line 101:
	**[http://www.wiwiss.fu-berlin.de/suhl/bizer/rdfapi/ RAP] - is a software package for parsing, searching, manipulating, serializing and serving RDF models.		**[http://www.wiwiss.fu-berlin.de/suhl/bizer/rdfapi/ RAP] - is a software package for parsing, searching, manipulating, serializing and serving RDF models.
	**[http://powl.sourceforge.net/ pOWL] - Semantic Web Development Platform - web-based ontology edititing and management solution		**[http://powl.sourceforge.net/ pOWL] - Semantic Web Development Platform - web-based ontology edititing and management solution
		+	**[http://arc.semsol.org/ ARC] - easy RDF and SPARQL for LAMP systems
		+	*Python
		+	**[http://rdflib.net/ RDFLib] - Python library for working with RDF ([http://wiki.python.org/moin/RdfLib RDFLib Wiki])
		+	**[http://oort.to/ Oort] - a Python toolkit for accessing RDF graphs as plain objects (it has RDFLib under the crust)
		+	**[http://www.mnot.net/sw/sparta/ 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.
		+	**[http://infomesh.net/pyrple/ Pyrple] - Python 2.3 RDF toolkit
	*Java code generators		*Java code generators
	**[http://rdfreactor.ontoware.org/ RDFReactor] views the RDF data model through object-oriented Java proxies; Java interfaces are generated automatically from an RDF Schema		**[http://rdfreactor.ontoware.org/ RDFReactor] views the RDF data model through object-oriented Java proxies; Java interfaces are generated automatically from an RDF Schema

Ilya: /* Servers */

2008-03-03T18:22:41Z

Servers

←Older revision		Revision as of 18:22, 3 March 2008
Line 52:		Line 52:
	*[http://arc.web-semantics.org/ 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.		*[http://arc.web-semantics.org/ 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.
	*[http://threestore.sourceforge.net/ 3store] - a C library that uses MySQL to store its raw RDF data and caches, part of the [http://www.aktors.org/akt/ AKT Project].		*[http://threestore.sourceforge.net/ 3store] - a C library that uses MySQL to store its raw RDF data and caches, part of the [http://www.aktors.org/akt/ AKT Project].
		+	*[http://rdfbroker.opendfki.de/ 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
	*[http://www.guha.com/rdfdb/ rdfDB]: An RDF Database		*[http://www.guha.com/rdfdb/ rdfDB]: An RDF Database
	*[http://rdfstore.sourceforge.net/ RDFStore] - Perl/C RDF storage and API		*[http://rdfstore.sourceforge.net/ RDFStore] - Perl/C RDF storage and API

Ilya: /* Companies */

2008-02-12T02:21:43Z

Companies

←Older revision		Revision as of 02:21, 12 February 2008
Line 271:		Line 271:
	*[http://www.powerset.com/ Powerset] - natural language search		*[http://www.powerset.com/ Powerset] - natural language search
	*[http://www.franz.com/ Franz Inc] develops [http://www.franz.com/products/allegrograph/ AllegroGraph] triple-store which works with [http://www.franz.com/products/racer/ RacerPro] reasoner and [http://www.topbraidcomposer.com/features.html TopBraid Composer] Semantic Web IDE		*[http://www.franz.com/ Franz Inc] develops [http://www.franz.com/products/allegrograph/ AllegroGraph] triple-store which works with [http://www.franz.com/products/racer/ RacerPro] reasoner and [http://www.topbraidcomposer.com/features.html TopBraid Composer] Semantic Web IDE
-	*[http://www.cambridgesemantics.com/ Cambridge Semantics] - middleware platforms	+	*[http://www.cambridgesemantics.com/ Cambridge Semantics] - middleware platforms ([http://www.cambridgesemantics.com/people/ people])

	</div>		</div>
	{{Synthetic biology bottom}}		{{Synthetic biology bottom}}

Ilya: /* Companies */

2008-02-12T02:19:40Z

Companies

←Older revision		Revision as of 02:19, 12 February 2008
Line 271:		Line 271:
	*[http://www.powerset.com/ Powerset] - natural language search		*[http://www.powerset.com/ Powerset] - natural language search
	*[http://www.franz.com/ Franz Inc] develops [http://www.franz.com/products/allegrograph/ AllegroGraph] triple-store which works with [http://www.franz.com/products/racer/ RacerPro] reasoner and [http://www.topbraidcomposer.com/features.html TopBraid Composer] Semantic Web IDE		*[http://www.franz.com/ Franz Inc] develops [http://www.franz.com/products/allegrograph/ AllegroGraph] triple-store which works with [http://www.franz.com/products/racer/ RacerPro] reasoner and [http://www.topbraidcomposer.com/features.html TopBraid Composer] Semantic Web IDE
		+	*[http://www.cambridgesemantics.com/ Cambridge Semantics] - middleware platforms

	</div>		</div>
	{{Synthetic biology bottom}}		{{Synthetic biology bottom}}

Ilya: /* Servers */

2008-01-11T00:24:48Z

Servers

←Older revision		Revision as of 00:24, 11 January 2008
Line 48:		Line 48:
	*[http://www.openrdf.org/ Sesame]: an open source RDF database with support for RDF Schema inferencing and querying		*[http://www.openrdf.org/ Sesame]: an open source RDF database with support for RDF Schema inferencing and querying
	**[http://www.ontotext.com/owlim/ OWLIM] - OWL Semantic Repository packaged as a Storage and Inference Layer (SAIL) for the Sesame RDF database		**[http://www.ontotext.com/owlim/ OWLIM] - OWL Semantic Repository packaged as a Storage and Inference Layer (SAIL) for the Sesame RDF database
-	*[http://kowari.org/ ~~kowari~~]: database for the storage, retrieval and analysis of RDF and OWL metadata; non-relational, written in Java.	+	*[http://kowari.org/ Kowari]: database for the storage, retrieval and analysis of RDF and OWL metadata; non-relational, written in Java.
		+	*[http://www.mulgara.org/ Mulgara] is a scalable RDF database written entirely in Java. Mulgara is an Open Source fork of [http://kowari.org/ Kowari].
	*[http://arc.web-semantics.org/ 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.		*[http://arc.web-semantics.org/ 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.
	*[http://threestore.sourceforge.net/ 3store] - a C library that uses MySQL to store its raw RDF data and caches, part of the [http://www.aktors.org/akt/ AKT Project].		*[http://threestore.sourceforge.net/ 3store] - a C library that uses MySQL to store its raw RDF data and caches, part of the [http://www.aktors.org/akt/ AKT Project].