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 …

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