Final version of my presentation to BioIT World Congress, Boston MA, April 22, 2010. Describes how we're using the SADI Semantic Web Service framework to begin personalizing medical research.

1. Research… this time it’s Personal! Mark Wilkinson, PI Bioinformatics, Heart + Lung Institute @ St. Paul’s Hospital Vancouver, BC, Canada

2. DEMO...to give you incentive to listen to the rest of the presentation ;-)

3. Show me patients with elevated creatinine along with their latest BUN and creatinine levels PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#> PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient rdf:typepatients:ElevatedCreatininePatient . ?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat . }

4. VOILA!

5. There was no database...There was no patient data anywhere annotated as “Elevated Creatinine Patient”

6. How did I answer a question where the required data didn’t exist? (...no, I didn’t just make it up! LOL!)

7. The story begins...

8. This is going to hurt...

9. Web Servicesvs.Semantic Web

10. Web Servicesare not “connected” to the Semantic WebWhy?

11. Web ServicesXML + XML SchemaSemantic WebRDF + OWL

12. Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML

13. Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics

14. Web Services&Semantic WebFundamentally and deeply different Web technologies!

16. >1000 X more data in the “Deep Web” than in Web pages

17. Accessing these databases and analytical algorithms “transparently”, based on an individual researcher’s ideas, beliefs, and preferenceswill help us personalize medical research

18. Mark Butler (2003) Is the semantic web hype? Hewlett Packard laboratories presentation at MMU, 2003-03-12

19. Semantic Web?(my definition) An information system where machines can receive information from one source, re-interpret it, and correctly use it for a purpose that the source had not anticipated.

20. Re-interpretation Correct re-use Both are critical to the personalization of research

21. Building a personalized Semantic Web… Step-by-step…

22. Semantic Automated Discovery and Integrationhttp://sadiframework.org(open source) MicrosoftResearch Founding partner

23. SADI“best-practices” for Semantic Web Service provision

24. standards-compliant

25. Lightweight(only 2 “rules”)

26. Rules come from observations:

27. SADI Observation #1: Web Services in Bioinformatics create implicitbiologicalrelationships between their input and output

28. SADI Observation #1:

29. SADI Best Practice #1 Make the implicit explicit… A Web Service should create “triples” linking the input data to the output data, thus explicitly describing the semantic relationship between them

30. SADI Best Practice #1 This is what bioinformatics Web Services implicitly do anyway! Easy to implement this as a best-practice

31. SADI Observation #2:HTTP GET and POST GET guarantees the response relates to the request URI in a very precise and predictable way POST does not…

32. SADI Observation #2:GET and POST That’s why Web Services have a fundamentally different behaviour than the Semantic Web

33. SADI Observation #2:GET and POST We can fix that! (without breaking any existing rules or standards!)

34. SADI Best Practice #2 SUBJECT URI of the output graph (triples) is the sameas the SUBJECT URI of the input graph (triples) (the output is “about” the input... Now explicitly!)

35. Consequence The “Semantics” of our interaction with the Web Service are now explicitandidentical to the “Semantics” of GET

36. SADI Web Service Interfaces Service Interfaces defined by two OWL classes:

37. SADI Web Service Interfaces OWL Class #1: My Input Class

38. SADI Web Service Interfaces OWL Class #2: My Output Class

39. SADI Web Service Interfaces My Service consumes OWL Individuals of Class #1and returns OWL Individuals of Class #2 …but the URI of those two individuals is the same!(see best practice #2)

40. How do we discover services? Since input and output are about the same “thing”, we can automatically determine what a service doesby comparing the Input and Output OWL classes

41. How do we discover services? Automatically index services in a registry based on what properties (predicates) Services add to their respective input data

42. EXAMPLE Input Data: BRCA1 rdf:type Gene ID Output Data: BRCA1 hasDNASequence AGCTTAGCCA… Registry Index: Service provides “hasDNASequence” property to Gene IDs

43. Now we can answer questions like “what is the DNA sequence of BRCA1?”  Discover a SADI Web Service that generates the DNA Sequence property for gene identifiers

44. Okay, enough tech gobbledygookWhat will this do for ME?

45. Demo #1

46. Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output ofevery conceivable analysis

47. How do we query that database?

48. “SHARE”Semantic Health And Research EnvironmentSADI client application

50. What pathways does UniProt protein P47989 belong to? PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> PREFIX ont: <http://ontology.dumontierlab.com/> PREFIX uniprot: <http://lsrn.org/UniProt:> SELECT ?gene ?pathway WHERE { uniprot:P47989 pred:isEncodedBy ?gene . ?gene ont:isParticipantIn ?pathway . }

54. Recapwhat we just saw A standard SPARQL query was entered into SHARE, a SADI-aware query engine

55. Recapwhat we just saw The query was interpreted to extract the properties being queried and these were passed to SADI for Web Service discovery

56. Recapwhat we just saw SADIsearched-for, found, and accessed all databases and/or analytical tools capable of generating those properties

57. Recapwhat we just saw We posed, and answered a complex database query WITHOUT A DATABASE (in fact, the data didn’t even have to exist...)

58. Cool!

59. …but I’m supposed to be personalizing research… Let’s make this a little more personal by bringing in Ontologies

60. My Definition of Ontology (for this talk) Ontologies explicitly define the things that exist in “the world” based on what propertieseach kind of thing must have

61. Ontology Spectrum Frames (Properties) Thesauri “narrower term” relation Selected Logical Constraints (disjointness, inverse, …) Catalog/ ID Formal is-a Informal is-a Formal instance General Logical constraints Terms/ glossary Value Restrs.

62. Demo #2 Discover instances of OWL classes from data that doesn’t exist…

63. Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatinine levels. PREFIX regress: <http://sadiframework.org/examples/regression.owl#> PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#> PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient patients:creatinineLevels ?collection . ?collection regress:hasRegressionModel ?model . ?model regress:slope ?slope FILTER (?slope > 0) . ?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat . }

67. Show me patients with elevated creatinine along with their latest BUN and creatinine levels PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#> PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient rdf:typepatients:ElevatedCreatininePatient . ?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat . }

68. Start burrowing through the OWL class  find that we need aregression model OWL class

69. Regression models have features like slopes and intercepts… and so onThe class is completely decomposed until a set of required Services are discoveredcapable of creating all these necessary properties

70. Successful decomposition of the OWL class to discover the need for a LinearRegression Web Service, and so on

71. VOILA!

72. OWL Class restrictions converted into workflows SPARQL queries converted into workflows Reasoning happening in parallel with query executionData fulfilling OWL models is discovered, or generated through running analytical tools SADI and CardioSHARE

73. I still don’t seewhy this is“Personal”??

74. Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatinine SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient rdf:typepatients:ElevatedCreatininePatient . ?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat . }

75. I created a small ontologydescribing my definition ofan Elevated Creatinine Patient

76. … it was MY ontology!

77. I can re-use it

78. I can modify it as I change myworld-view

79. I can publish it for others to use

80. Others can modify it to fit THEIRworld-view

82. My personal world-view is being dynamically resolved againstglobal data and knowledge

83. …but it’s bigger than that…

84. “Elevated Creatinine Patient”

85. I made that up! It came out of my head!

86. What’s a fancy word for a world-view that you make-up? Hypothesis

87. Current Research We believe that ontologies and hypothesesare, in some ways, the same “thing”……simply assertions about individuals that may or may not existFuture SADI client applications will supportdata-driven hypothesis generation and resolution

88. Recap SADI Semantic Web Services generate triples; the predicates of those triples are indexed... Period. For a given query, determine which properties are available, and which need to be discovered/generated Find services that generate the properties we need

89. Semantic Web An information system where machines can receive information from one source, re-interpret it, and correctly use it for a purpose that the source had not anticipated. My Purpose!!

90. What SADI + SHARE supports Re-interpretation We constantly compare the collection of properties, gathered from third-parties worldwide, to whatever world-model (query/ontology) we wish to view it through. MY world model

91. What SADI + SHARE supports Novel re-use There is no way for the provider to dictate how their data should be used, or how it should be interpreted. They simply add their properties into the “data cloud” and those properties are used in whatever way is appropriate forME.

92. And all this because SADI simply requires that the input URI is the same as the output URI

93. Semi-automated SADI service writing and deployment Taverna Semantically-guided SADI service discovery and pipelining SADI Plug-ins

94. Simple and Open WINS! Join us! We have recently received funding from CANARIEto assist and train service providersin deploying their own SADI Semantic Web Services Come join us – we’re having a lot of fun!! http://sadiframework.org http://twitter.com/sadiframework

95. Credits Benjamin VanderValk (SADI & CardioSHARE) Luke McCarthy (SADI & CardioSHARE) SoroushSamadian (CardioSHARE) Microsoft Research Fin This presentation available on SlideShare: keywords ‘wilkinson’ ‘BioIT-2010’

96. Credits Benjamin VanderValk(SADI & CardioSHARE) Luke McCarthy (SADI & CardioSHARE) SoroushSamadian(CardioSHARE)

97. Microsoft Research