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Web 2.0 + Web 3.0 = Web 5.0?

Web 2.0 + Web 3.0 = Web 5.0?. The HSFBCY + CIHR + Microsoft Research SADI and CardioSHARE Projects Mark Wilkinson Heart + Lung Research Institute iCAPTURE Centre, St. Paul’s Hospital, UBC. “Non-logical” reasoning and SPARQL queries over distributed data that doesn’t exist.

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Web 2.0 + Web 3.0 = Web 5.0?

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  1. Web 2.0 + Web 3.0 = Web 5.0? The HSFBCY + CIHR + Microsoft Research SADI and CardioSHARE Projects Mark Wilkinson Heart + Lung Research Institute iCAPTURE Centre, St. Paul’s Hospital, UBC

  2. “Non-logical” reasoning and SPARQL queries over distributed data that doesn’t exist

  3. How do we make data and tools easily available to biologists

  4. Ontologies!

  5. Problem…

  6. Ontology Spectrum Because it fulfils XXX WHY? 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. Because I say so! Originally from AAAI 1999- Ontologies Panel by Gruninger, Lehmann, McGuinness, Uschold, Welty; – updated by McGuinness. Description in: www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-abstract.html

  7. 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

  8. 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.

  9. My goal with this talk:the “sweet spot”

  10. COST 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.

  11. COMPREHENSIBILITY 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.

  12. Likelihood of being “right” 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.

  13. Here’s my argument…

  14. 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.

  15. Semantic Web? If we cannot achieve those two things, then IMO we don’t have a “semantic web”, we only have a distributed (??), linked database… and that isn’t particularly exciting or interesting…

  16. Where is the semantic web? 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. REASON: “Because I say so” is not open to re-interpretation

  17. Founding partner

  18. SADI Premise #1:Web Services in Bioinformatics expose the implicit biological relationship between an input and its associated output

  19. SADI Premise #1:

  20. SADI Premise #2:A web services registry that provides WS discovery based on these properties enables the behaviours expected of the Semantic Web

  21. DynamicDistributedDiscoveryInterpretationRe-interpretation

  22. Example SADI-enabled AppImagine: there exists a “virtual graph” connecting every conceivable input to every conceivable Web Service and their respective outputs... How do we query that graph?

  23. DEMO “SHARE”A SADI-enabled query resolver for life sciences

  24. Recapwhat we just saw A SPARQL database query was entered into the SHARE environment The query was passed to SADI and was interpreted based on the properties being asked-about SADI searched-for, found, and accessed the databases and/or analytical tools required to generate those properties

  25. Recapwhat we just saw We asked, and answered a complex “database query” WITHOUT A DATABASE

  26. Founding partner

  27. CardioSHARE A domain-specific implementation of SADI Utilizes OWL ontologies describing cardiovascular concepts Ontologies are designed to lie in the “sweet spot” of the Semantic range

  28. CardioSHARE Premise #1:Ontology = Query = Workflow

  29. QUERY: SELECT images of mutations from genes in organism XXX that share homology to this gene in organism YYY Concept: “Homologous Mutant Image” WORKFLOW

  30. Phrased in terms of properties: SELECT image P where { Gene Q hasImage image P Gene Q hasSequence Sequence Q Gene R hasSequence Sequence R Sequence Q similarTo Sequence R Gene R = “my gene of interest” }

  31. …but these are simply axioms… HomologousMutantImage is equivalentTo { Gene Q hasImage image P Gene Q hasSequence Sequence Q Gene R hasSequence Sequence R Sequence Q similarTo Sequence R Gene R = “my gene of interest” }

  32. Class: homologous mutant images

  33. QUERY: Retrieve homologous mutant images for gene XXX

  34. CardioSHARE We are not building massive ontologies! Publish small, independent single-Classes of OWL Cheap Scalable Flexible Don’t try to describe all of biology!

  35. DEMO CardioSHARE

  36. Recap SADI interprets queries (SPARQL + OWL Class Definitions) Determine which properties are available, and which need to be discovered/generated Discovery of services via on-the-fly “classification” of local data with small OWL Classes representing service interfaces

  37. Recap CardioSHARE encapsulates workflows as OWL ClassesOntology = Query = Workflow Ontologies consist of one class Low-cost, high accuracy

  38. CardioSHARE OWL Classes are shared on the Web such that third-parties, potentially with different expertise, can utilize the expertise of the person who designed the Class. Easily share your expertise with others Easily utilize the expertise of others ...all based on the premise that we define the world by its properties, rather than its classes

  39. CardioSHARE repercussion... if Ontology = query = workflowandquery = hypothesisthenOntology = Hypothesis

  40. Currrent Research How far can we push theOntology = Hypothesisapproach??Attempting to duplicate some clinical outcomes research using ONLY ontologies

  41. What we achieve Re-interpretation : The SADI data-store simply collects properties, and matches them up with OWL Classes in a SPARQL query and/or from individual service provider’s WS interface

  42. What we achieve Novel re-use: Because we don’t pre-classify, there is no way for the provider to dictate how their data should be used. They simply add their properties into the “cloud” and those properties are used in whatever way is appropriate for me.

  43. What we achieve Data remains distributed – no warehouse! Data is not “exposed” as a SPARQL endpoint  greater provider-control over computational resources Yet data appears to be a SPARQL endpoint… no modification of SPARQL or reasoner required. No longer dependent on “pure” DL logic

  44. Credits Edward Kawas and ~40 others (Moby) Benjamin VanderValk (SADI & SHARE) Luke McCarthy (SADI & SHARE) SoroushSamadian (CardioSHARE) Maria Markov & VeronikaGrandl(CardioSHARE “dumb” data model) MicrosoftResearch O | B | F Fin

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