http://www.pcworld.idg.com.au/article/132245/berners-lee_seeks_killer_app_semantic_web "Similarly, if we could get critical mass in life sciences, if we get a half a dozen or a dozen set of ontologies, the core ones for drug discovery out there, then suddenly the Semantic Web within life sciences would have a critical mass. It'll snowball much more rapidly and it will be copied. Other areas will realize: Oh it's worth investing in this," Tim Berners-Lee WWW inventor
The problem: How to do data integration in Bioinformatics ? Carole Goble (ISWC 2005)
"Wouldn't it be great if you were able to organize all this information based on your own terms, instead of based on the application you use to access the information ?” Ramanathan V. Guha RDF initiator http://cgi.netscape.com/columns/techvision/innovators_rg.html
Bio2RDF Mouse and Human Atlas map in 2008 65 millions triples
Linked Data cloud evolution http://linkeddata.org/ http://esw.w3.org/topic/TaskForces/CommunityProjects/LinkingOpenData/DataSets/Statistics Linked data cloud in March 2009 Linked data cloud in May 2007
Namespace resolution through DNS subdomain </li></ul>
Bio2RDF has 3 mirror sites http://cu.bio2rdf.org/ http://qut.bio2rdf.org/ http://quebec.bio2rdf.org/
Main REST services <ul><li>Describe a ressource by a dereferencable URI </li><ul><li>http://bio2rdf.org/ ns : id </li></ul><li>Global services over federated endpoints </li><ul><li>http://bio2rdf.org/links/ ns : id
http://bio2rdf.org/search/ searchedTerm </li></ul><li>Targeted services to a specific endpoint </li><ul><li>http://bio2rdf.org/linksns/ ns2 / ns : id
The mashup principle To answer a complex question we first need to build a specific database, a mashup, to which we submit the appropriate query.
Cognoscope new definition <ul>A Cognoscope is an instrument to explore and collect topics from the Linked Data cloud of SPARQL endpoints. It permits the querying over a distributed network of knowledge resource. </ul>
Cognoscope definition <ul><li>The magnifying effect depends of the density of links between resource (entity links), which is a by-product of the human intellectual activity in the social network.
The filtering effect is based on the inherent semantic of RDF graph described using types and predicates.
Facet browsing is used to zoom in and out in the observed graph.
Full text search is used to discover concept. </li></ul>
Cognoscope function <ul><li>How can we submit a complex query over the network of SPARQL endpoints ? </li><ul><li>By using a workflow fetching individual SPARQL endpoints. </li></ul><li>We use a workflow to build the mashup. </li></ul>
Bio2RDF Cognoscope architecture Linked Data cloud of SPARQL endpoints Triplestore Virtuoso 6 Workflow engine Taverna 2.1
By building a mashup with Taverna <ul><li>Write your complex SPARQL query as if a global graph would be available
Identify the needed namespaces and split the query to fetch each data source separetly
Build a mashup using a Taverna workflow that instanciate a local triplestore
Execute your complex query locally on the mashup </li></ul>
The SPARQL query needed (dont try this home, do it on the web !)