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SADI: Semantic Support for Automated Workflow GenerationThe SADI Taverna plugin and SHARE<br />Presentation to Workflow tr...
Web ServicesXML + XML SchemaSemantic WebRDF + OWL<br />
Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML<br />
Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics<br />
Web Services&Semantic WebFundamentally and deeply different Web technologies! <br />
How can we make them work together?<br />
Semantic Automated Discovery and Integrationhttp://sadiframework.org<br />MicrosoftResearch<br />Founding partner<br />
SADI“best-practices” for Semantic Web Service provision<br />
standards-compliant<br />
Lightweight(only 2 “rules”)<br />
What [most] bioinformatics Web Services do<br />HTTP   POST<br />RESPONSE<br />
Bioinformatics web services implicitlycreate RDF “triples”<br />
SADI “rule” #1<br />Make the implicit explicit…<br />A Web Service should create RDF “triples” linking input and output da...
SADI Rule #2<br />(Simple derivation from rule #1)<br />The URI of the inputmust be preserved in the output<br />Therefore...
Consequence<br />The “Semantics” of our <br />interaction with the Web Service are now<br />explicit <br />
Consequence<br />“Semantics” of HTTP POST are identical to the “Semantics” of HTTP GET<br />Therefore SADI Web Services <b...
IMPORTANT!!<br />SADI concerns itself ONLY with the way Web Services themselves are modeled<br />SADI is not competitive w...
Taverna<br />A workbench for designing and executingScientific Workflows<br />
Load-up your data and press “play”!<br />
SADI Plug-in to Taverna<br />
KEGG_Pathway<br />KEGG Record<br />hasPathwayGene<br />
Initialize Semantic Search...<br />
Connect your desired service to the workflow<br />
Lather, Rinse, Repeat<br />
And so on<br />Und so weiter<br />
Because we’re generating RDFthe output data is often in the form of a URI<br />
And these URIs are “Live”<br />
SADI-Taverna Summary<br />Search for the property of the data you desire<br />Automatically adds the service<br />correctl...
SHARESemantic Health And Research Environment<br />SPARQL enhanced by SADI<br />
A  Novel SPARQL Query Engine<br />Uses SADI to automatically construct a workflow that creates a query-specific database<b...
Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants<br />...
Likely Rejecter:<br />A patient who has creatinine levelsthat are increasing over time<br />- - Wilkinson MD<br />
Likely Rejecter:<br />…but there is no “likely rejecter” column or table in our database… only blood chemistry measurement...
?<br />
The definition of a LikelyRejecter is encoded in a machine-readable document  written in the OWL language  (“Ontology”)<br...
The machine continues to burrow down through the definition and discovers that regression lines have things like slopes an...
Then… <br />Two magical events occur…<br />
The machine figures out<br />by itselfthe need to do a Linear Regression analysisin order to answer your question<br />
The machine figures out<br />by itselfhow and wherethat analysiscan be doneand does it automatically!<br />
http://www.impactlab.net/2009/03/22/improve-your-brain-power/<br />
The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis<br />
VOILA!<br />
SHARE Summary<br />SADI -enabled fully automated workflow generationin the context of creating a database capable of answe...
Join us!<br />SADI and CardioSHARE are Open-Source projects<br />Come join us – we’re having a lot of fun!!<br />http://sa...
 Credits<br />Benjamin VanderValk(SHARE & SADI)<br />Luke McCarthy (SADI, SHARE, Taverna, CardioSHARE)<br />SoroushSamadia...
U of New Brunswick<br />Dr. Chris BakerAlexandreRiazanov<br />Carleton University<br />Dr. Michel Dumontier<br />	Marc-Ale...
Microsoft Research<br />
Fin<br />This presentation available on SlideShare:  keywords   ‘wilkinson’   ‘ISoLA2010’<br />
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ISoLA 2010: SADI Taverna plug-in

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Presentation to the workflow track of ISoLA 2010, Crete. Includes explanation of the SADI plug-in to Taverna, and how the SHARE client automatically constructs and semantic web service workflow to answer specific sparql queries.

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Transcript of "ISoLA 2010: SADI Taverna plug-in"

  1. 1. SADI: Semantic Support for Automated Workflow GenerationThe SADI Taverna plugin and SHARE<br />Presentation to Workflow track<br />ISoLA 2010, Crete, October 2010<br />
  2. 2. Web ServicesXML + XML SchemaSemantic WebRDF + OWL<br />
  3. 3. Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML<br />
  4. 4. Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics<br />
  5. 5. Web Services&Semantic WebFundamentally and deeply different Web technologies! <br />
  6. 6. How can we make them work together?<br />
  7. 7. Semantic Automated Discovery and Integrationhttp://sadiframework.org<br />MicrosoftResearch<br />Founding partner<br />
  8. 8. SADI“best-practices” for Semantic Web Service provision<br />
  9. 9. standards-compliant<br />
  10. 10. Lightweight(only 2 “rules”)<br />
  11. 11. What [most] bioinformatics Web Services do<br />HTTP POST<br />RESPONSE<br />
  12. 12. Bioinformatics web services implicitlycreate RDF “triples”<br />
  13. 13. SADI “rule” #1<br />Make the implicit explicit…<br />A Web Service should create RDF “triples” linking input and output data, thus explicitly describing the semantic relationship between them<br />Input and output structuresdescribed by OWL Classes<br />
  14. 14. SADI Rule #2<br />(Simple derivation from rule #1)<br />The URI of the inputmust be preserved in the output<br />Therefore, the output is explicitly about the input<br />
  15. 15. Consequence<br />The “Semantics” of our <br />interaction with the Web Service are now<br />explicit <br />
  16. 16. Consequence<br />“Semantics” of HTTP POST are identical to the “Semantics” of HTTP GET<br />Therefore SADI Web Services <br />behave like the Semantic Web<br />
  17. 17. IMPORTANT!!<br />SADI concerns itself ONLY with the way Web Services themselves are modeled<br />SADI is not competitive with<br />nor incompatible with*<br />existing Web Service description standards<br />(OWL-S, WSDL2, etc.)<br />* AFAIK<br />
  18. 18. Taverna<br />A workbench for designing and executingScientific Workflows<br />
  19. 19.
  20. 20. Load-up your data and press “play”!<br />
  21. 21. SADI Plug-in to Taverna<br />
  22. 22.
  23. 23.
  24. 24. KEGG_Pathway<br />KEGG Record<br />hasPathwayGene<br />
  25. 25. Initialize Semantic Search...<br />
  26. 26. Connect your desired service to the workflow<br />
  27. 27.
  28. 28. Lather, Rinse, Repeat<br />
  29. 29.
  30. 30. And so on<br />Und so weiter<br />
  31. 31.
  32. 32.
  33. 33.
  34. 34. Because we’re generating RDFthe output data is often in the form of a URI<br />
  35. 35. And these URIs are “Live”<br />
  36. 36. SADI-Taverna Summary<br />Search for the property of the data you desire<br />Automatically adds the service<br />correctly connected automatically<br />Unlike earlier BioMobyplugin, the SADI plugin handles parsing into and out of RDF format automatically and transparently<br />Easy to connect SADI with non-SADI services<br />
  37. 37. SHARESemantic Health And Research Environment<br />SPARQL enhanced by SADI<br />
  38. 38. A Novel SPARQL Query Engine<br />Uses SADI to automatically construct a workflow that creates a query-specific database<br />
  39. 39. Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants<br />PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> <br />PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> <br />PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> <br />SELECT ?patient ?bun ?creat<br />FROM <http://sadiframework.org/ontologies/patients.rdf><br />WHERE {<br /> ?patientrdf:typepatient:LikelyRejecter .<br /> ?patient l:latestBUN ?bun . <br /> ?patient l:latestCreatinine ?creat . <br />}<br />
  40. 40. Likely Rejecter:<br />A patient who has creatinine levelsthat are increasing over time<br />- - Wilkinson MD<br />
  41. 41. Likely Rejecter:<br />…but there is no “likely rejecter” column or table in our database… only blood chemistry measurementsat various time-points<br />
  42. 42. ?<br />
  43. 43. The definition of a LikelyRejecter is encoded in a machine-readable document written in the OWL language (“Ontology”)<br />“the regression line over creatinine measurements should have an increasing slope”<br />
  44. 44. The machine continues to burrow down through the definition and discovers that regression lines have things like slopes and intercepts, etc…<br />
  45. 45. Then… <br />Two magical events occur…<br />
  46. 46. The machine figures out<br />by itselfthe need to do a Linear Regression analysisin order to answer your question<br />
  47. 47. The machine figures out<br />by itselfhow and wherethat analysiscan be doneand does it automatically!<br />
  48. 48. http://www.impactlab.net/2009/03/22/improve-your-brain-power/<br />
  49. 49. The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis<br />
  50. 50. VOILA!<br />
  51. 51. SHARE Summary<br />SADI -enabled fully automated workflow generationin the context of creating a database capable of answering<br />A SPARQL query<br />Data absent from local data-store automatically determined to be neededand the necessary workflow automatically constructed<br />
  52. 52. Join us!<br />SADI and CardioSHARE are Open-Source projects<br />Come join us – we’re having a lot of fun!!<br />http://sadiframework.org<br />
  53. 53. Credits<br />Benjamin VanderValk(SHARE & SADI)<br />Luke McCarthy (SADI, SHARE, Taverna, CardioSHARE)<br />SoroushSamadian(CardioSHARE)<br />David Withers(Taverna)<br />Edward Kawas(SADI Service auto-generator)<br />
  54. 54. U of New Brunswick<br />Dr. Chris BakerAlexandreRiazanov<br />Carleton University<br />Dr. Michel Dumontier<br /> Marc-Alexandre Nolin<br /> Leonid Chepelev<br /> Steve Etlinger<br />NichaellaKieth<br /> Jose Cruz<br />
  55. 55. Microsoft Research<br />
  56. 56. Fin<br />This presentation available on SlideShare: keywords ‘wilkinson’ ‘ISoLA2010’<br />
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