How SADI & SHARE help restore the Scientific Method to in silico science
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This 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 how SADI allows complex queries to be answered by discovering and executing relevant web services without a centralized database. The author's vision is for SADI to support the scientific method by enabling personal ontologies and hypotheses to be explicitly expressed and evaluated dynamically.
![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.](https://image.slidesharecdn.com/bosc20102-100707114525-phpapp02/85/How-SADI-SHARE-help-restore-the-Scientific-Method-to-in-silico-science-6-320.jpg)
![Holy Grail Demo #1Align 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.](https://image.slidesharecdn.com/bosc20102-100707114525-phpapp02/85/How-SADI-SHARE-help-restore-the-Scientific-Method-to-in-silico-science-22-320.jpg)
![Holy Grail Demo #2Align 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.](https://image.slidesharecdn.com/bosc20102-100707114525-phpapp02/85/How-SADI-SHARE-help-restore-the-Scientific-Method-to-in-silico-science-30-320.jpg)
How SADI & SHARE help restore the Scientific Method to in silico science
- 1. From BioMoby to SADIThe 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 registryGenome Canada, SUN Center of Excellence, CalgaryGenome España, Barcelona Supercomputing CenterInternational Rice Research Institute, Philippines Max Planck, CologneCanadian service registry brokers ~400,000 requests/monthCanadian BioMoby services receive ~700,000 uses/monthCanadian 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, SaskatchewanSept 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.
- 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 sawA standard SPARQL query was entered into SHARE, a SADI-aware query engine
- 17. Recapwhat we just sawThe query was interpreted to extract the “triple” patternssubject, predicate, objectbeing requested
- 18. Recapwhat we just sawTriple-patterns are passed to SADI for Web Service discovery
- 19. Recapwhat we just sawServices capable of generating those triple-patterns are automatically executed, the triples are stored, and the query is resolved.
- 20. Recapwhat we just sawWe posed, and answered a ~complex database query WITHOUT A DATABASE(in fact, the data didn’t even have to exist...)
- 21. Recapwhat we just sawNote that there is no centralized ontologyUnlike BioMoby, SADI supports all (OWL) ontologiesand does not invent any of its own
- 22. Holy Grail Demo #1Align 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 transplantsPREFIX 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 ?creatFROM <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 #2Align 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 servicesTaverna
- 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 ManifestoWhat is my next “Holy Grail”?
- 35. ScienceSupport for the in silicoScientific Method
- 37. The Scientific MethodDiscourse: 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 doReproducibility: This is how I did it (“provenance”)Clarity: This is my new hypothesis
- 38. The Scientific MethodDiscourse: 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 doReproducibility: This is how I did it (“provenance”)Clarity: This is my new hypothesisWorkflows (e.g. myExperiment)
- 40. In opposition to the lessons we learnt from Web 2.0The Semantic Web in Healthcare and Life Sciencesis solving the problems of science……by forming institutions
- 41. Result:Large, centrally-designed and centrally-curated ontologies that enforce“community agreement” about “biological reality”
- 47. To bring the “traditions of Science” to in silicoScienceWeb 3.0 must 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 ?creatFROM <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
- 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 Classis 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 validityHypothesisIschemiaSADI+ SHAREHypertensionBlood PressureAnalytical AlgorithmDatabase 1Database 2
- 69. Join us!SADI and CardioSHARE are Open-Source projectsCome join us – we’re having a lot of fun!!http://sadiframework.orgSADI 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 providersWe can help you get started!“C-BRASS” is on Facebook!Like
- 71. CreditsBenjamin VanderValk(SADI & SHARE)Luke McCarthy (SADI & SHARE)SoroushSamadian(CardioSHARE)