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SHARE & the Semantic Web — This Time it's Personal

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Luke McCarthy

1. The document describes the Semantic Automated Discovery and Integration (SADI) framework for building semantic web services. 2. In SADI, a service is identified by a URI and responds to GET requests with a service description and to POST requests by taking RDF input and producing RDF output. 3. SADI services define input and output classes in OWL that describe the expected input and generated output so that services can be discovered based on semantic types.

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SHARE & the Semantic Web This Time it’s Personal! http:// sadiframework.org
SADI Semantic Automated Discovery & Integration (Semantic Web Services)
A SADI service… … is identified by a URI also an HTTP URL http://sadiframework.org/examples/hello
A SADI service… … responds to GET with service description RDF document describing the service URI conforms to Feta (BioMoby, myGrid) <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mygrid="http://www.mygrid.org.uk/mygrid-moby-service#"> <mygrid:serviceDescription rdf:about="http://sadiframework.org/examples/hello"> <mygrid:hasServiceNameText rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello</mygrid:hasServiceNameText> <mygrid:hasServiceDescriptionText>A simple "Hello</mygrid:hasServiceDescriptionText> <mygrid:hasOperation> <mygrid:operation rdf:about="http://sadiframework.org/examples/hello#operation"> <mygrid:outputParameter> <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#output"> <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#GreetedIndividual"/> </mygrid:parameter>
A SADI service… … responds to POST with service output RDF in, RDF out <hello:NamedIndividual rdf:about="http://sadiframework.org/examples/hello-input.rdf#1"> <foaf:name>Guy Incognito</foaf:name> </hello:NamedIndividual> <hello:GreetedIndividual rdf:about="http://sadiframework.org/examples/hello-input.rdf#1"> <hello:greeting>Hello, Guy Incognito!</hello:greeting> </hello:GreetedIndividual>
A SADI service… <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mygrid="http://www.mygrid.org.uk/mygrid-moby-service#"> <mygrid:serviceDescription rdf:about="http://sadiframework.org/examples/hello"> <mygrid:hasServiceNameText rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello</mygrid:hasServiceNameText> <mygrid:hasServiceDescriptionText>A simple "Hello</mygrid:hasServiceDescriptionText> <mygrid:hasOperation> <mygrid:operation rdf:about="http://sadiframework.org/examples/hello#operation"> <mygrid:inputParameter> <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#input"> http://sadiframework.org/examples/hello.owl#NamedIndividual <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#NamedIndividual"/> </mygrid:parameter> </mygrid:inputParameter> <mygrid:outputParameter> http://sadiframework.org/examples/hello.owl#GreetedIndividual <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#output"> <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#GreetedIndividual"/> </mygrid:parameter> </mygrid:outputParameter> </mygrid:operation> </mygrid:hasOperation> </mygrid:serviceDescription> </rdf:RDF>
A SADI service… … has an input OWL class describes the RDF it consumes property restrictions characterize the data it needs <owl:Class rdf:ID="NamedIndividual"> <owl:equivalentClass> <owl:Restriction> http://xmlns.com/foaf/0.1/name <owl:onProperty rdf:resource="http://xmlns.com/foaf/0.1/name"/> <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</owl:minCardinality> </owl:Restriction> </owl:equivalentClass> </owl:Class>
A SADI service… … has an output OWL class describes the RDF it produces property restrictions characterize the data it provides <owl:Class rdf:ID="GreetedIndividual"> <owl:equivalentClass> <owl:Restriction> http://sadiframework.org/examples/hello.owl#greeting <owl:onProperty rdf:resource="#greeting"/> <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</owl:minCardinality> </owl:Restriction> </owl:equivalentClass> </owl:Class>
SHARE & the Semantic Web — This Time it's Personal
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:regress="http://sadiframework.org/examples/regression.owl#"> <regress:PairedValueCollection rdf:about="http://sadiframework.org/examples/input1"> <regress:element> <regress:PairedValue> <regress:x rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</regress:x> <regress:y rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</regress:y> </regress:PairedValue> </regress:element> <regress:element> <regress:PairedValue> <regress:x rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</regress:x> <regress:y rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</regress:y> </regress:PairedValue> </regress:element> </regress:PairedValueCollection> </rdf:RDF> #1 Service <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:regress="http://sadiframework.org/examples/regression.owl#"> <regress:OutputClass rdf:about="http://sadiframework.org/examples/input1"> <regress:hasRegressionModel> <regress:LinearRegressionModel> #1 <regress:intercept rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.5</regress:intercept> <regress:slope rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.5</regress:slope> </regress:LinearRegressionModel> </regress:hasRegressionModel> </regress:OutputClass> </rdf:RDF> Client # #1
OWL classes in SADI… … are local to individual services one service’s world-view can conflict with another, but a client can use both not dogmatically; some types are shared (e.g. database records) … use global properties maximize interoperability represent community agreement
Input OWL classes in SADI… … are dynamically assignable property restrictions are sufficient for membership another way to discover services: what can I get with what I have now?
There’s nothing to it.
SHARE Semantic Health And Research Environment
• SPARQL engine • triple patterns are matched against service descriptions • knowledge base is dynamically populated • queries can contain OWL classes, which are expanded to the required triple patterns • query is optimized to minimize the number of service calls and the amount of data sent over the network
PREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#> PREFIX dumontier: <http://ontology.dumontierlab.com/> PREFIX kegg: <http://lsrn.org/KEGG_PATHWAY:> SELECT ?gene ?protein ?seq WHERE { kegg:hsa00232 dumontier:hasParticipant ?gene . ?gene sadi:encodes ?protein . ?protein sadi:hasSequence ?seq } Service Service Service
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi }
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi } 1. initialize an empty knowledge base backed by an OWL reasoner 2. load URLs in FROM clauses http://biordf.net/cardioSHARE/patients.rdf <rdf:Description rdf:ID="patient6"> <mged:has_height> <mged:Measurement> <mged:has_units rdf:resource="&mged;m"/> <mged:has_value>1.8034</mged:has_value> </mged:Measurement> </mged:has_height> <mged:has_mass> <mged:Measurement> <mged:has_units rdf:resource="&mged;kg"/> <mged:has_value>73.9355563</mged:has_value> </mged:Measurement> </mged:has_mass> <rdfs:label>patient #6</rdfs:label> <rdfs:comment>I am not a number, I am a free man!</rdfs:comment> </rdf:Description>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi } 3. select next triple pattern ?patient rdf:type patients:AtRiskPatient 4. process pattern
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . } ?patient bmi:BMI ?x } 5. decompose OWL class http://biordf.net/cardioSHARE/patients.owl#AtRiskPatient <owl:Class rdf:ID="AtRiskPatient"> <rdfs:label>A patient at risk for some condition</rdfs:label> <owl:equivalentClass> <owl:Restriction> <owl:onProperty rdf:resource="&bmi;BMI"/> BMI some double[> 25] <owl:someValuesFrom> <rdfs:Datatype> <owl:onDatatype rdf:resource="&xsd;double"/> <owl:withRestrictions rdf:parseType="Collection"> <rdf:Description> <xsd:minExclusive rdf:datatype="&xsd;double">25</xsd:minExclusive> </rdf:Description> </owl:withRestrictions> </rdfs:Datatype> </owl:someValuesFrom> </owl:Restriction> </owl:equivalentClass> </owl:Class>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 6. select next triple pattern ?patient bmi:BMI ?bmi 7. process pattern
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 8. find services that attach the predicate bmi:BMI → http://sadiframework.org/examples/calculateBMI 9. find inputs to service use ?patient candidates no candidates; find instances of the service’s input class http://sadiframework.org/examples/bmi.owl#InputClass filter inputs previously sent to this service
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 10.invoke the service assemble minimal RDF that still satisfies the input class POST that RDF and add the response to the KB 11.update variable candidates use current triple pattern
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 12.select next triple pattern ?patient bmi:BMI ?x 13.process pattern
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 14.find services that attach the predicate bmi:BMI → http://sadiframework.org/examples/calculateBMI 15.find inputs to service use ?patient candidates filter inputs previously sent to this service nothing to do
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 16.select next triple pattern no more patterns 17.execute original SPARQL query using the populated knowledge base and a conventional SPARQL reasoner
OWL classes in SHARE queries… … are personal but defined in terms of common properties … are shared class URIs resolve to their definitions anyone can use your class with their data … are flexible disagree with a definition? try a new one!
OWL classes in SHARE queries… … are workflows describe the data that’s needed, not the services to call (though the service chain can be reconstructed) … are hypotheses? “what is” → “what might be”
Acknowledgements This research is supported by The Heart + Stroke Foundation of BC and Yukon, Microsoft Research, The Canadian Institutes of Health Research, The Natural Sciences and Engineering Research Council of Canada and CANARIE.

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SHARE & the Semantic Web — This Time it's Personal

  • 1. SHARE & the Semantic Web This Time it’s Personal! http:// sadiframework.org
  • 2. SADI Semantic Automated Discovery & Integration (Semantic Web Services)
  • 3. A SADI service… … is identified by a URI also an HTTP URL http://sadiframework.org/examples/hello
  • 4. A SADI service… … responds to GET with service description RDF document describing the service URI conforms to Feta (BioMoby, myGrid) <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mygrid="http://www.mygrid.org.uk/mygrid-moby-service#"> <mygrid:serviceDescription rdf:about="http://sadiframework.org/examples/hello"> <mygrid:hasServiceNameText rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello</mygrid:hasServiceNameText> <mygrid:hasServiceDescriptionText>A simple "Hello</mygrid:hasServiceDescriptionText> <mygrid:hasOperation> <mygrid:operation rdf:about="http://sadiframework.org/examples/hello#operation"> <mygrid:outputParameter> <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#output"> <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#GreetedIndividual"/> </mygrid:parameter>
  • 5. A SADI service… … responds to POST with service output RDF in, RDF out <hello:NamedIndividual rdf:about="http://sadiframework.org/examples/hello-input.rdf#1"> <foaf:name>Guy Incognito</foaf:name> </hello:NamedIndividual> <hello:GreetedIndividual rdf:about="http://sadiframework.org/examples/hello-input.rdf#1"> <hello:greeting>Hello, Guy Incognito!</hello:greeting> </hello:GreetedIndividual>
  • 6. A SADI service… <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mygrid="http://www.mygrid.org.uk/mygrid-moby-service#"> <mygrid:serviceDescription rdf:about="http://sadiframework.org/examples/hello"> <mygrid:hasServiceNameText rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello</mygrid:hasServiceNameText> <mygrid:hasServiceDescriptionText>A simple "Hello</mygrid:hasServiceDescriptionText> <mygrid:hasOperation> <mygrid:operation rdf:about="http://sadiframework.org/examples/hello#operation"> <mygrid:inputParameter> <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#input"> http://sadiframework.org/examples/hello.owl#NamedIndividual <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#NamedIndividual"/> </mygrid:parameter> </mygrid:inputParameter> <mygrid:outputParameter> http://sadiframework.org/examples/hello.owl#GreetedIndividual <mygrid:parameter rdf:about="http://sadiframework.org/examples/hello#output"> <mygrid:objectType rdf:resource="http://sadiframework.org/examples/hello.owl#GreetedIndividual"/> </mygrid:parameter> </mygrid:outputParameter> </mygrid:operation> </mygrid:hasOperation> </mygrid:serviceDescription> </rdf:RDF>
  • 7. A SADI service… … has an input OWL class describes the RDF it consumes property restrictions characterize the data it needs <owl:Class rdf:ID="NamedIndividual"> <owl:equivalentClass> <owl:Restriction> http://xmlns.com/foaf/0.1/name <owl:onProperty rdf:resource="http://xmlns.com/foaf/0.1/name"/> <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</owl:minCardinality> </owl:Restriction> </owl:equivalentClass> </owl:Class>
  • 8. A SADI service… … has an output OWL class describes the RDF it produces property restrictions characterize the data it provides <owl:Class rdf:ID="GreetedIndividual"> <owl:equivalentClass> <owl:Restriction> http://sadiframework.org/examples/hello.owl#greeting <owl:onProperty rdf:resource="#greeting"/> <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</owl:minCardinality> </owl:Restriction> </owl:equivalentClass> </owl:Class>
  • 10. <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:regress="http://sadiframework.org/examples/regression.owl#"> <regress:PairedValueCollection rdf:about="http://sadiframework.org/examples/input1"> <regress:element> <regress:PairedValue> <regress:x rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</regress:x> <regress:y rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</regress:y> </regress:PairedValue> </regress:element> <regress:element> <regress:PairedValue> <regress:x rdf:datatype="http://www.w3.org/2001/XMLSchema#int">3</regress:x> <regress:y rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</regress:y> </regress:PairedValue> </regress:element> </regress:PairedValueCollection> </rdf:RDF> #1 Service <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:regress="http://sadiframework.org/examples/regression.owl#"> <regress:OutputClass rdf:about="http://sadiframework.org/examples/input1"> <regress:hasRegressionModel> <regress:LinearRegressionModel> #1 <regress:intercept rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.5</regress:intercept> <regress:slope rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.5</regress:slope> </regress:LinearRegressionModel> </regress:hasRegressionModel> </regress:OutputClass> </rdf:RDF> Client # #1
  • 11. OWL classes in SADI… … are local to individual services one service’s world-view can conflict with another, but a client can use both not dogmatically; some types are shared (e.g. database records) … use global properties maximize interoperability represent community agreement
  • 12. Input OWL classes in SADI… … are dynamically assignable property restrictions are sufficient for membership another way to discover services: what can I get with what I have now?
  • 14. SHARE Semantic Health And Research Environment
  • 15. • SPARQL engine • triple patterns are matched against service descriptions • knowledge base is dynamically populated • queries can contain OWL classes, which are expanded to the required triple patterns • query is optimized to minimize the number of service calls and the amount of data sent over the network
  • 16. PREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#> PREFIX dumontier: <http://ontology.dumontierlab.com/> PREFIX kegg: <http://lsrn.org/KEGG_PATHWAY:> SELECT ?gene ?protein ?seq WHERE { kegg:hsa00232 dumontier:hasParticipant ?gene . ?gene sadi:encodes ?protein . ?protein sadi:hasSequence ?seq } Service Service Service
  • 17. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi }
  • 18. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi } 1. initialize an empty knowledge base backed by an OWL reasoner 2. load URLs in FROM clauses http://biordf.net/cardioSHARE/patients.rdf <rdf:Description rdf:ID="patient6"> <mged:has_height> <mged:Measurement> <mged:has_units rdf:resource="&mged;m"/> <mged:has_value>1.8034</mged:has_value> </mged:Measurement> </mged:has_height> <mged:has_mass> <mged:Measurement> <mged:has_units rdf:resource="&mged;kg"/> <mged:has_value>73.9355563</mged:has_value> </mged:Measurement> </mged:has_mass> <rdfs:label>patient #6</rdfs:label> <rdfs:comment>I am not a number, I am a free man!</rdfs:comment> </rdf:Description>
  • 19. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi } 3. select next triple pattern ?patient rdf:type patients:AtRiskPatient 4. process pattern
  • 20. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . } ?patient bmi:BMI ?x } 5. decompose OWL class http://biordf.net/cardioSHARE/patients.owl#AtRiskPatient <owl:Class rdf:ID="AtRiskPatient"> <rdfs:label>A patient at risk for some condition</rdfs:label> <owl:equivalentClass> <owl:Restriction> <owl:onProperty rdf:resource="&bmi;BMI"/> BMI some double[> 25] <owl:someValuesFrom> <rdfs:Datatype> <owl:onDatatype rdf:resource="&xsd;double"/> <owl:withRestrictions rdf:parseType="Collection"> <rdf:Description> <xsd:minExclusive rdf:datatype="&xsd;double">25</xsd:minExclusive> </rdf:Description> </owl:withRestrictions> </rdfs:Datatype> </owl:someValuesFrom> </owl:Restriction> </owl:equivalentClass> </owl:Class>
  • 21. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 6. select next triple pattern ?patient bmi:BMI ?bmi 7. process pattern
  • 22. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 8. find services that attach the predicate bmi:BMI → http://sadiframework.org/examples/calculateBMI 9. find inputs to service use ?patient candidates no candidates; find instances of the service’s input class http://sadiframework.org/examples/bmi.owl#InputClass filter inputs previously sent to this service
  • 23. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 10.invoke the service assemble minimal RDF that still satisfies the input class POST that RDF and add the response to the KB 11.update variable candidates use current triple pattern
  • 24. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 12.select next triple pattern ?patient bmi:BMI ?x 13.process pattern
  • 25. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 14.find services that attach the predicate bmi:BMI → http://sadiframework.org/examples/calculateBMI 15.find inputs to service use ?patient candidates filter inputs previously sent to this service nothing to do
  • 26. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://biordf.net/cardioSHARE/patients.owl#> PREFIX bmi: <http://sadiframework.org/examples/bmi.owl#> SELECT ?patient ?bmi FROM <http://biordf.net/cardioSHARE/patients.rdf> WHERE { ?patient rdf:type patients:AtRiskPatient . ?patient bmi:BMI ?bmi . ?patient bmi:BMI ?x } 16.select next triple pattern no more patterns 17.execute original SPARQL query using the populated knowledge base and a conventional SPARQL reasoner
  • 27. OWL classes in SHARE queries… … are personal but defined in terms of common properties … are shared class URIs resolve to their definitions anyone can use your class with their data … are flexible disagree with a definition? try a new one!
  • 28. OWL classes in SHARE queries… … are workflows describe the data that’s needed, not the services to call (though the service chain can be reconstructed) … are hypotheses? “what is” → “what might be”
  • 29. Acknowledgements This research is supported by The Heart + Stroke Foundation of BC and Yukon, Microsoft Research, The Canadian Institutes of Health Research, The Natural Sciences and Engineering Research Council of Canada and CANARIE.

Editor's Notes

  • #11: *make it obvious the input and output node are the same(with animation or label)*