The document discusses the transition from BioMoby to SADI as a framework for semantic web services. It provides statistics on BioMoby usage and describes demonstrations of complex queries being answered through SADI and SHARE without a centralized database. The demonstrations include finding pathways for a protein and lab results for transplant patients. It advocates for SADI to support the scientific method and personal hypotheses through distributed ontologies rather than centralized ones.

1. From BioMoby to SADI The Quest for the Holy Grail!

2. BioMoby Stats in a nutshell >1800 servicesworldwide (~1300 “alive” at any given time) 4 major installations of the Moby Service registry Genome Canada, SUN Center of Excellence, Calgary Genome España, Barcelona Supercomputing Center International Rice Research Institute, Philippines Max Planck, Cologne Canadian service registry brokers ~400,000 requests/month Canadian BioMoby services receive ~700,000 uses/month Canadian server just had a significant memory upgrade to improve performance “The report of my death was an exaggeration” -- Mark Twain

3. Model Organism Bring Your-Own Database Interface Conference “MOBY-DIC” Emma Lake, Saskatchewan Sept 21, 2001

5. Are we going after The Holy Grail here?

6. The Holy Grail:(this slide created circa 2002) Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels. Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.

7. http://sadiframework.org MicrosoftResearch Founding partner

8. Holy Grail Demo #1

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

10. How do we query that database?

11. “SHARE”Semantic Health And Research EnvironmentSADI client applicationhttp://biordf.net/cardioSHARE (Pellet)http://dev.biordf.net/cardioSHARE (Pellet 2)

12. 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 . }

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

17. Recapwhat we just saw The query was interpreted to extract the “triple” patterns subject, predicate, objectbeing requested

18. Recapwhat we just saw Triple-patterns are passed to SADI for Web Service discovery

19. Recapwhat we just saw Services capable of generating those triple-patterns are automatically executed, the triples are stored, and the query is resolved.

20. 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...)

21. Recapwhat we just saw Note that there is no centralized ontologyUnlike BioMoby, SADI supports all (OWL) ontologies and does not invent any of its own

22. Holy Grail Demo #1 Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels. Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.

23. Holy Grail Demo #2

24. Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient rdf:typepatient:LikelyRejecter . ?patient l:latestBUN ?bun . ?patient l:latestCreatinine ?creat . }

25. Start burrowing through the LikelyRejector OWL class  find that we need a regression model OWL class

26. Regression models have features like slopes and intercepts, and so on.The class is completely decomposed until a set of required Services are discoveredcapable of creating all these necessary properties

27. Decomposition of the OWL class uncovers the need for a Linear Regression analysis on the patient blood chemistry data

28. VOILA!

29. We just dynamically evaluated if individuals matching a particular high-level concept definition exist…or can exist

30. Holy Grail Demo #2 Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels. Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.

31. How does SADI + SHARE do that?

32. Please see other presentations uploaded to SlideShare for a full explanation of SADI Functionality See also the Taverna and Protégé plug-insfor discovering, running and creating services Sentient Knowledge Explorer Taverna

33. The Holy Grail may not yet be in-handbut I think we can at least see it from here!So… now what?

34. Mark’s Manifesto What is my next “Holy Grail”?

35. Science Support for the in silico Scientific Method

37. The Scientific Method Discourse: What do you believe? What do I believe? Disagreement: You’re wrong! And I’m gonna prove it! Clarity: This is the experiment I am going to do Reproducibility: This is how I did it (“provenance”) Clarity: This is my new hypothesis

38. The Scientific Method Discourse: What do you believe? What do I believe? Disagreement: You’re wrong! And I’m gonna prove it! Clarity: This is the experiment I am going to do Reproducibility: This is how I did it (“provenance”) Clarity: This is my new hypothesis Workflows (e.g. myExperiment)

40. In opposition to the lessons we learnt from Web 2.0 The Semantic Web in Healthcare and Life Sciencesis currently solving the problems of science… …by forming institutions

41. Result: Large, centrally-designed and centrally-curated ontologies that enforce “community agreement” about “biological reality”

42. Science ≠ Consensus

47. To bring the “traditions of Science” to in silicoScience we need Web 3.0 tools that encourage and facilitate personalopinionand debate

48. What has this got to do with SADI and SHARE?

49. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creat FROM <http://sadiframework.org/ontologies/patients.rdf> WHERE { ?patient rdf:typepatient:LikelyRejecter . ?patient l:latestBUN ?bun . ?patient l:latestCreatinine ?creat . }

50. Likely Rejecter

51. Icreated a small ontologydescribing my definition ofa Likely Rejecter

52. … it was MY ontology!

53. I can re-use it

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

55. I can publish it for others to use

56. Others can modify it and/or compare it to THEIR world-view

57. Sharing my ontology also gives opportunities for micro-attribution;“Citation” of me is transparent and automatic when someone extends my ontology

58. Using SADI and SHAREmypersonal world-view isexplicitlyexpressedand can bedynamically evaluated againstglobal data and knowledge

59. Ontology development is distributed and personalrather than centralized no institutions“an ecosystem of ideas!”

61. …but there’s more…

62. “Likely Rejecter”

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

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

65. The “Likely Rejecter” OWL Class is an explicitly-expressed hypothesis; Members of that class may or may not exist!

68. Ontologically-expressed Hypotheses drive the discovery, assembly, and analysis of data capable of evaluating their validity Hypothesis Ischemia SADI + SHARE Hypertension Blood Pressure Analytical Algorithm Database 1 Database 2

69. Join us! SADI and CardioSHARE are Open-Source projects Come join us – we’re having a lot of fun!! http://sadiframework.org SADI SemanticWeb Services Page #SADIFramework

70. C-BRASS: Canadian Bioinformatics Resources As Semantic Servicestogether with Michel Dumontier, Chris Baker ~$1M funding to help us deploy SADI services and provide training for new service providers We can help you get started! “C-BRASS” is on Facebook! Like

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

72. Microsoft Research

73. Credits Benjamin VanderValk (SADI & CardioSHARE) Luke McCarthy (SADI & CardioSHARE) SoroushSamadian (CardioSHARE) IO Informatics (Knowledge Explorer API) Microsoft Research Fin This presentation available on SlideShare: keywords ‘wilkinson’ ‘bosc’