Log of 2010-03-12

• ​http://www.semantic-systems-biology.org/biogateway/querying  
• ​http://www.semantic-systems-biology.org/biogateway/sparql-viewer/#app=dfd3&dd55-selectedIndex=0&e98b-selectedIndex=0
• Mapping RDF to Java
• * "TOOLS: If you are intrigued and would like to investigate the possibilities of expanding your OOP world with semantic technologies there are several open source tools available today. I’ve divided them up into two major categories; Annotation based tools which take advantage of Java’s inherent annotation feature to bind to RDF and Code generators, which generate java code based on a given OWL or RDF schema document."
  • ​http://www.semanticuniverse.com/articles-binding-java-objects-rdf.html
• Other ways to run sparql :
  • sparql implementations ​http://esw.w3.org/topic/SparqlImplementations
  • ​http://semanticweb.org/sparql/
  • ​http://www4.wiwiss.fu-berlin.de/is-group/snorql/
  • ​http://sparql.sourceforge.net/
  • ​http://semantic-mediawiki.org/wiki/Help:SPARQL_endpoint
  • ​Download virtuoso
    • ​http://download.openlinksw.com/downwiz/#cliv
• ​Skos is the area of work developing specification and standard to support the use of knowledge . Encodes in RDF towards interoperability and easy publication of controlled structured vocabularies.
• java generator - mapping file :tutorial how to create a genarator inside molgenis :
  • in molgenis distro --> new package --> new class that extends generator: /molgenis/src/org/molgenis/generators/mygenerator/StuffGen.java ( this class extend ForEachEntityGenarator? created inside Molgenis.
  • You need here function generate (but it is already creted in ForEachEntityGenarator? which extend genarator )
    • public void generate(Model model, MolgenisOptions? options) throws Exception {

creates the templates : it gets the extension and from the xml model file it gets the entities (for (Entity entity : model.getEntities()) { )...--> This generated the templates which are located in ( ? )/molgenis_distro/generated/java/addressbook/mygenerator

• ...so what you actually need to write is
  • getdescription ..which returns a description
  • getPackage import /includes ... anything else ??? staff you may need like? (mapping files?)

• why to create a mapping file :
  • "Since the Java language uses a different set of data types than Virtuoso a type mapping system has been established to allow the passage of data to and from Java."
  • virtuoso & java generator : ​http://docs.openlinksw.com/virtuoso/javaextvm.html

So probably we'll need a lot of them --> here comes the generator (see above)

• How to include virtuoso in molgenis?? as a service ??
  • ​http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VOSSparqlProtocol

• How to actually call sparql: ​http://www.w3.org/TR/rdf-sparql-protocol/#query-bindings-http

!LinkS/TutoRials

• open data spaces : ​http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/OdsIndex
  • ​http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/OdsIndex
  • ​http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/OdsFramework
  • ​http://en.wikipedia.org/wiki/OpenLink_Data_Spaces
• virtuoso products
  • ​http://www.slideshare.net/rumito/virtuoso-universal-server-overview-presentation
• sPARql:
  • ​http://jena.sourceforge.net/ARQ/Tutorial/
  • ​http://www.ibm.com/developerworks/xml/library/j-sparql/
• sparql @virtuoso
  • ​http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VOSODSSparqlSamples
    • ​http://demo.openlinksw.com/
• virtuoso & java genarator : ​http://docs.openlinksw.com/virtuoso/javaextvm.html
• linked data ​http://linkeddata.org/
• virtuoso sponger is and RDFizer..converts data to RDF: (RDF proxy server : e.g. ​http://demo.openlinksw.com/proxy/rdf/http://www.w3.org/People/Berners-Lee/card)
  • ​http://www.slideshare.net/rumito/virtuoso-sponger-rdfizer-middleware-for-creating-rdf-from-non-rdf-data-sources
  • ​http://virtuoso.openlinksw.com/presentations/Virtuoso_Sponger_1/Virtuoso_Sponger_1.html#(3)