SADI SWSIP '09 'cause you can't always GET what you want!
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The document discusses the differences between web services and the semantic web, emphasizing how existing web services lack rigorous semantics compared to the flexible semantics offered by the semantic web. It introduces the SADI framework, which aims to enhance web services with rich semantics to make them compatible with the semantic web's requirements, focusing on creating explicit biological relationships and enabling discovery through a novel prototyping method. The text outlines various observations and demonstrations of SADI's capabilities in integrating and querying data across distributed systems while maintaining provider control over resources.
![BACKGROUND of DATASETNIST toxicity compendium study 8 toxicantsLiverSerumUrineGenomic [Affymetrix MA]Metabolomic [LC/MS] dataconducted under NIST Advanced Technology Program (ATP), Award # 70NANB2H3009 as a Joint Venture between Icoria / Cogenics (Division of CLDA) and IO Informatics.](https://image.slidesharecdn.com/sadiswsip09-091206220242-phpapp01/85/SADI-SWSIP-09-cause-you-can-t-always-GET-what-you-want-34-320.jpg)
SADI SWSIP '09 'cause you can't always GET what you want!
- 1. ’cause you can’t always GET what you want!
- 3. Web Servicesare not “connected” to the Semantic WebWhy?
- 4. Web ServicesXML + XML SchemaSemantic WebRDF + OWL
- 5. Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML
- 6. Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics
- 7. Web Services&Semantic Web Fundamentally different technologies!
- 9. >1000 X more data in the Deep Web than in Web pagesIn bioinformatics this is primarily databases and analytical algorithms
- 10. Web Service output is criticalto success for the Semantic Web!!
- 12. WITHOUT INVENTING A NEW TECHNOLOGY OR STANDARD
- 13. Can we define frameworks and/or best practices that make Web Services “transparent” to the Semantic Web?
- 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…
- 16. What do we need to do?Make Web Services exhibit the same “behavior” as GETAdd rich Semantics to Web Services at every level of the WS “stack”
- 17. What do we have to work with?(Without inventing new technologies or standards…)DataInterface annotations
- 18. Semantic Automated Discovery and Integrationhttp://sadiframework.orgFounding partner
- 19. History of SADIBased on observations of the usage and behaviour of BioMoby Semantic Web Servicessince 2002
- 20. SADI Observation #1:What does ‘GET’ really do? What “behaviour” of GET do we need to mimic in a Web Service?
- 21. SADI Observation #1:GET guarantees the response relates to the input URI in a very precise and predictable wayPOST does not…Web Services have a fundamentally different semantic behaviour than the Semantic Web
- 22. SADI Observation #1:We can fix that!(without breaking any existing rules or standards!)
- 23. SADI Observation #2:All Web Services in Bioinformatics create implicitbiologicalrelationships between their input and output
- 25. SADI: Core PropositionMake the implicit explicitModel all Web Services this way
- 26. SADI: Core PropositionWeb Service output must be TriplesSUBJECT URI of the output graph is the same URI as the SUBJECT URI of the input graphthat was POSTedto the Web ServiceDefine OWL classes that describe your input and output triples
- 27. Consequence(i.e. why SADI works!)The Semantics of the triples from a Web Service are now explicit and identical to the Semantics of GET
- 28. How do we exploit this?Current Web Service definition systems such as WSDL, and OWL-S are missing a crucial annotation element……the semantic relationship between input and output
- 29. How do we exploit this?With SADI services, this relationship can be automatically derived by “diff-ing” the input and output OWL classes…because the SUBJECT node of the input and output graphs is guaranteed to be the same!
- 30. How do we exploit this?We have constructed a simple prototype Web Services registry that provides discovery based on annotation of these biological relationships
- 31. Demo #1a plug-in to the IO-Informatics Knowledge Explorer
- 32. The Sentient Knowledge Explorerfrom IO InformaticsA Semantic Integration, Visualization and Search Tool
- 33. SADI Plug-in to the Sentient Knowledge ExplorerThe Knowledge Explorer has a plug-ins API that we have utilized to pass data directly from SADI to the KE visualization and exploration systemData elements in KE are queried for their “type” (rdf:type); this is used to discover additional data properties by querying the SADI Web Service registry
- 34. BACKGROUND of DATASETNIST toxicity compendium study 8 toxicantsLiverSerumUrineGenomic [Affymetrix MA]Metabolomic [LC/MS] dataconducted under NIST Advanced Technology Program (ATP), Award # 70NANB2H3009 as a Joint Venture between Icoria / Cogenics (Division of CLDA) and IO Informatics.
- 35. Microarray studies were conducted under NIEHS contract # N01-ES-65406.
- 36. The Alcohol study was conducted under NIAAA contract # HHSN281200510008C in collaboration with Bowles Center for Alcohol Studies (CAS) at UNC.
- 37. This work was also made possible through contributions from members of IO Informatics’ Working Group on “Semantic Applications for Translational Research”.DEMOKnowledge ExplorerPlug-inFor more information about the Knowledge Explorer surf to:http://io-informatics.com
- 42. Call SADI to provide discovery of predicates based on data-type
- 44. SADI fills-in the “Encodes” property from the discovered Web Service(s)
- 46. Discover services that provide the hasGOTerm property for Protein Sequence datatype
- 48. DEMOKnowledge ExplorerPlug-inFor more information about the Knowledge Explorer surf to:http://io-informatics.com
- 49. SADI Demo #2Imagine there is a “virtual graph” connecting every conceivable input for every conceivable Web Service to their respective outputs How do we query that graph?
- 50. “SHARE”Semantic Health And Research EnvironmentSADI client application
- 52. 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 . }
- 56. Recapwhat we just sawA standard SPARQL query was entered into SHARE – a SADI-based query engineThe query was interpreted to extract the properties being queried and these were passed to SADI for Web Service discoverySADI searched-for, found, and accessed the databases and/or analytical tools capable of generating those properties
- 57. Recapwhat we just sawWe posed, and answered a complex database query WITHOUT A DATABASE(in fact, the data didn’t even have to exist...)
- 58. RDF graph browsing and querying is useful… …but where’s the semantics??Let’s bring in some ontologies!
- 59. 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
- 60. Ontology SpectrumFrames(Properties)Thesauri“narrowerterm”relationSelectedLogical Constraints(disjointness, inverse, …) Catalog/IDFormalis-aInformalis-aFormalinstanceGeneralLogicalconstraintsTerms/glossaryValue Restrs.
- 61. 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.
- 63. Powered by SADIPrototype SADI-enabled SWS Client
- 64. Data exhibits “late binding”
- 65. Late binding:“purpose and meaning” of the data isnot determined untilthe moment it is required
- 66. Benefitof late bindingData is amenable toconstant re-interpretation
- 67. How do we achieve this?DO NOT PRE-CLASSIFY DATA!just hang properties on it
- 68. These are axioms that enable classificationFrames(Properties)Thesauri“narrowerterm”relationSelectedLogical Constraints(disjointness, inverse, …) Catalog/IDFormalis-aInformalis-aFormalinstanceGeneralLogicalconstraintsTerms/glossaryValue Restrs.These are indexing/annotation systems
- 69. Design OWL-DL ontologies describing cardiovascular conceptsOntologies are in the “Frames+” area of the Ontology spectrum, and therefore can leverage SADI and be “executed” as workflows
- 70. What the…??? Did you just say “execute ontologies as workflows?!”
- 71. Another interesting consequence of the SADI architectureOntology = Query = Workflow
- 73. WORKFLOW
- 74. QUERY:SELECT images of mutations from genes in organism XXX that share homology to this gene in organism YYY
- 76. As OWL AxiomsHomologousMutantImage is owl:equivalentTo {Gene Q hasImage image PGene Q hasSequence Sequence QGene R hasSequence Sequence R Sequence Q similarTo Sequence RGene R = “my gene of interest” }
- 77. Those axioms combine to create an OWL Class:homologous mutant images
- 78. QUERY:Retrieve owl:homologous mutant images for gene XXX
- 79. Demo #3Discover instances of OWL classes from data that doesn’t exist…
- 80. 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 ?creatFROM <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 . }
- 84. Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatininelevels(now as an OWL class ElevatedCreatininePatient)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 ?creatFROM <http://sadiframework.org/ontologies/patients.rdf>WHERE { ?patient rdf:typepatients:ElevatedCreatininePatient . ?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat . }
- 85. Start burrowing through the OWL class find that we need aregression model OWL class
- 86. 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
- 87. Successful decomposition of the OWL class to discover the need for a LinearRegression Web Service, and so on
- 88. VOILA!
- 89. Demo #3Discover instances of OWL classes from data that doesn’t exist…
- 90. SADI and CardioSHAREOWL Class restrictions converted into workflowsSPARQL queries converted into workflowsReasoning happening at the same time as queries are being executed
- 91. (AFAIK)This is a completely novel behaviour!
- 92. Ontologies are reasonedWorkflows are executedQueries are resolvedso what do we call what this client does??
- 93. “Reckoning”Dynamic discovery of instances of OWL classes through synthesis and invocation of a Web Service workflow capable of generating data described by the OWL Class restrictions, followed by reasoning to classify the data into that ontology
- 94. But OWL Classes can be (and often are) completely “made-up”What does that mean in the context of SADI and CardioSHARE?
- 95. Current Research We believe that ontologies and hypothesesare, in some ways, the same “thing”……simply assertions about individuals that may or may not existIf an instance of a class exists, then the hypothesis is “validated”
- 96. Current Research Constructing OWL classes that represent patient categories mimicking clinical outcomes research experiments done on the BC Cardiac RegistryThe original experiments have already been published, and therefore act as a gold-standardWe attempt to use “Reckoning” to automatically discover instances of these patient Classes and compare our results with those of the clinical researchers
- 98. HypothesisIschemiaSADIWeb “agents”HypertensionBlood PressureCardioSHARE architecture: Increasingly complex ontological layers organize data into richer concepts, even hypothesesDatabase 1Database 2AnalysisAlgorithmXX
- 99. RecapSADI 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/generatedDiscovery of services through index queries + on-the-fly “classification” of local data against the service interface OWL Classes
- 100. Semantic WebAn 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.
- 101. What SADI + SHARE supportsRe-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 Web Service interface
- 102. What SADI + SHARE supportsNovel 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.
- 103. Important “wins”Data remains distributed – no warehouse!Data is not “exposed” as a SPARQL endpoint greater provider-control over computational resourcesYet data appears to be a SPARQL endpoint… no modification of SPARQL or reasoner required.
- 104. And all this because we simply require that the input URI is the same as the output URI
- 105. Join us!SADI and CardioSHARE are Open-Source projectsCome join us – we’re having a lot of fun!!http://sadiframework.org