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CSHALS 2010 W3C Semanic Web Tutorial
The document provides an overview of semantic web technologies and their application in fields like drug discovery and life sciences. It discusses the integration of disparate data sources through standards like RDF and SPARQL to enable effective data querying and interoperability. Additionally, it highlights the challenges in implementing these technologies, including a shortage of skilled professionals and the need for clear messaging.
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CSHALS 2010 W3C Semanic Web Tutorial
- 1.The Semantic WebLandscapeA Practical IntroductionLee FeigenbaumVP Technology & Standards, Cambridge SemanticsCo-chair, W3C SPARQL Working GroupFor CSHALS 2010 Tutorial AttendeesFebruary 24, 2010
- 2.The W3C HCLSinterest group set out to use Semantic Web technologies to receive precise answers to a complex question:A Motivating Example: Drug DiscoveryFind me genes involved in signal transduction that are related to pyramidal neurons.
- 3.General search223,000 hits,0 results
- 4.
- 5.
- 6.A Semantic WebApproachIntegrate disparate databases…MeSHPubMedEntrez GeneGene Ontology…
- 7.A Semantic WebApproach (cont’d)…so that onequery…
- 8.A Semantic WebApproach (cont’d)…(trivially) spans several databases…
- 9.A Semantic WebApproach (cont’d)…to deliver targeted results…
- 10.Agreement on commonterms and relationshipsIncremental, flexible data structureGood-enough modelingQuery interface tailored to the data modelWhat’s the trick?
- 11.What is thesemantic web?
- 12.
- 13.Semantic WebWeb ofDataGiant Global GraphData WebWeb 3.0Linked Data WebSemantic Data WebBranding
- 14.“The Semantic Web”a.k.a “Linked Open Data”Augments the World Wide WebRepresents the Web’s information in a machine-readable fashionEnables……targeted search…data browsing…automated agentsWhat is it & why do we care? (1)World Wide Web : Web pages :: The Semantic Web : Data
- 15.“Semantic Web technologies”Afamily of technology standards that ‘play nice together’, including:Flexible data modelExpressive ontology languageDistributed query languageDrive Web sites, enterprise applicationsWhat is it & why do we care? (2)The technologies enable us to build applications and solutions that were not possible, practical, or feasible traditionally.
- 16.A common setof technologies:...enables diverse uses...encourages interoperabilityA coherent set of technologies:…encourage incremental application…provide a substantial base for innovationA standard set of technologies:...reduces proprietary vendor lock-in...encourages many choices for tool setsA Common & Coherent Set of Technology Standards
- 17.
- 18.Semantic Web TechnologyTimeline200120042008201020071999RIFHCLS
- 19.As technologies &tools have evolved, Semantic Web advocates have progressed through stages:2010: Where we are
- 20.2010: Where we’renotImage from Trey Ideker via Enoch HuangSemantic Web technologies are not a ‘magic crank’ for discovering new drugs (or solving other problems, for that matter)!
- 21.2010: Where we’renot (cont’d)XML vs. RDF?“Ontology” vs. “ontology”?Data integration vs. reasoning vs. KBs vs. search vs. app. development vs. …Semantic Web vs. Linked Data?The Semantic Web still suffers from confusing and conflicting messaging, each of which asserts it’s “correct”.
- 22.2010: Where we’renot (cont’d)People with appropriate skill sets for designing & building Semantic Web solutions are not widely available.
- 23.2010: Where we’renot (cont’d)We don’t yet have standard solutions for privacy, trust, probability, and other elements of the Semantic Web vision.
- 24.What do SemanticWeb solutions look like?
- 25.RDF is…Resource DescriptionFramework
- 26.RDF is…The datamodel of the Semantic Web.
- 27.RDF is…A schema-lessdata model that features unambiguous identifiers and named relations between pairs of resources.
- 28.RDF is…A labeled,directed graph of relations between resources and literal values.RDF graphs are collections of triplesTriples are made up of a subject, a predicate, and an objectResources and relationships are named with URIspredicatesubjectobject
- 29.“Lee Feigenbaum worksfor Cambridge Semantics”“Lee Feigenbaum was born in 1978”“Cambridge Semantics is headquartered in Massachusetts”Example RDF triplesworks forborn inheadquarteredLee FeigenbaumCambridge SemanticsLee FeigenbaumCambridge Semantics1978Massachusetts
- 30.Triples connect toform graphsheadquarteredlives inMassachusettsborn incapitalworks forLee FeigenbaumCambridge SemanticsBoston1978
- 31.The graph datastructure makes merging datawith shared identifiers trivialTriples act as a least common denominatorfor expressing dataURIs for naming remove ambiguity…the same identifier means the same thingWhy RDF? What’s different here?
- 32.Why RDF? IncrementalIntegrationRelationalDatabaseRDF
- 33.RDF is themodel, for which there are several concrete syntaxes:RDF/XML – standard, complex XML syntaxTurtle – common, textual, triples-oriented syntaxN3 – more expressive superset of TurtleN-Triples – textual, line-oriented, useful for streamingWhat does RDF look like?When writing RDF by hand and in many guides, examples, and discussions these days, you’ll see Turtle most often.
- 34.Write a tripleby writing its parts separated by spaces (subject predicate object)A Bit of Turtle@prefix ex: <http://example.org/myvocab/> .@prefix geo: <http://geonames.example/> .ex:LeeFeigenbaumex:employerex:CambridgeSemantics .ex:LeeFeigenbaumex:birthYear 1978 .ex:CambridgeSemanticsex:headquartersgeo:BostonMA .geo:BostonMAex:population 574000 .
- 35.SPARQL is…SPARQL ProtocolAnd RDF Query Language
- 36.SPARQL is…The querylanguage of the Semantic Web.
- 37.SPARQL is…A SQL-likelanguage for querying sets of RDF graphs.
- 38.SPARQL is…A simpleprotocol for issuing queries and receiving results over HTTP. So…Every SPARQL client works with every SPARQL server!
- 39.SPARQL lets us:Pullinformation from structured and semi-structured data.Explore data by discovering unknown relationships.Query and search an integrated view of disparate data sources.Glue separate software applications together by transforming data from one vocabulary to another.Why SPARQL?
- 40.Dealer 1Dealer 2Dealer3EmployeeDirectoryERP / BudgetSystemWebEPA Fuel EfficiencySpreadsheetSPARQL Query EngineWhat automobiles get more than 25 miles per gallon, fit within my department’s budget, and can be purchased at a dealer located within 10 miles of one of my employees?SELECT ?automobileWHERE { ?automobile a ex:Car ; epa:mpg ?mpg ;ex:dealer ?dealer . ?employee a ex:Employee ; geo:loc ?loc . ?dealer geo:loc ?dealerloc . FILTER(?mpg > 25 && geo:dist(?loc, ?dealerloc) <= 10) .}Web dashboardSPARQL query
- 41.bio2rdf.org – queryinglife sciences data
- 42.bio2rdf.org – queryinglife sciences data
- 43.3 pieces ofthe Semantic Web technology stack are about describing a domain well enough to capture (some of) the meaning of resources and relationships in the domainRDF SchemaOWLRIFFrom the explicit to the inferredApply knowledge to data to get more data.
- 44.
- 45.Elements of:Vocabulary (definingterms)I define a relationship called “prescribed dose.”Schema (defining types)“prescribed dose” relates “treatments” to “dosages”(my prescribed dose is 2mg; therefore 2mg is a dosage)Taxonomy (defining hierarchies)Any “doctor” is a “medical professional”(therefore Dr. Brown is a medical professional)RDF Schema is…
- 46.WOL OWL is…WebOntology Language
- 47.Elements of ontologySame/differentidentity“author” and “auteur” are the same relationtwo resources with the same “ISBN” are the same “book”More expressive type definitionsA “cycle” is a “vehicle” with at least one “wheel”A “bicycle” is a “cycle” with exactly two “wheels”More expressive relation definitions“sibling” is a symmetric predicatethe value of the “favorite dwarf” relation must be one of “happy”, “sleepy”, “sneezy”, “grumpy”, “dopey”, “bashful”, “doc”OWL is…
- 48.A class isa (named) collection of things with similar attributesOWL: Rich Class Definitions
- 49.A class isa (named) collection of things with similar attributesOWL: Rich Class Definitions
- 50.A class isa (named) collection of things with similar attributesOWL: Rich Class Definitions
- 51.OWL: Rich ClassDefinitions
- 52.RIF is…Rules InterchangeFormat
- 53.Standard representation forexchanging sets of logical and business rulesLogical rulesA buyer buys an item from a seller if the seller sells the item to the buyerA customer becomes a "Gold" customer as soon as his cumulative purchases during the current year top $5000Production rulesCustomers that become "Gold" customers must be notified immediately, and a golden customer card will be printed and sent to them within one weekFor shopping carts worth more than $1000, "Gold" customers receive an additional discount of 10% of the total amountRIF is…
- 54.Fantasy Land ArchitectureOntology/ Schema+Custom UICustom UICustom UICustom UICustom UICustom UI
- 55.RealityInternetDB2XMLLDAP DirectoryOracleRDBCustom UICustomUICustom UICustom UICustom UICustom UI
- 56.GRDDL is…Gleaning ResourceDescriptions from Dialects of Language
- 57.GRDDL is…A methodfor authoritatively getting RDF data from XML and XHTML documents.
- 58.GRDDL is…A mechanismfor authoritatively deriving RDF data from families of XML and XHTML documents.
- 59.
- 60.RDB2RDF is…A W3CWorking Group to define a standard way to map from relational databases to RDF (and SPARQL).
- 61.A simple setof 4 guidelines for publishing RDF data on the Web (over HTTP)Developed by Tim Berners-Lee in 2006Use URIs as names for thingsGlobally unique identityUse HTTP URIs Everyone has a Web browser/clientWhen someone looks up a URI, provide useful information…in the form of RDF dataInclude links to other URIsFoster discovery of additional informationLinked Data is…
- 62.The LOD “cloud”,March 2009
- 63.Application specific portionsof the cloudNotably, bio-related data sets (in light purple)
- 64.some by theW3C “Linking Open Drug Data” task forceRDFa is…RDF in Attributes
- 65.RDFa is…A collectionof HTML attributes that allow RDF to be embedded directly in Web pages.
- 66.Don’t Repeat Yourself(DRY)In-context metadata (copy & paste)Authoritative (no screen scrapig)Why RDFa?
- 67.
- 68.
- 69.Semantic Web ToolsIn2010, there are a wide variety of open-source and commercial Semantic Web tools available.
- 70.Triple storesBuilt onrelational databaseNative RDF storeDevelopment librariesFull-featured application serversTypes of RDF ToolsMost RDF tools contain some elements of each of these.
- 71.Community-maintained listshttp://esw.w3.org/topic/SemanticWebToolsEmphasis onlarge triple storeshttp://esw.w3.org/topic/LargeTripleStoresMichael Bergman’s Sweet Tools searchable list:http://www.mkbergman.com/?page_id=325Finding RDF Tools
- 72.Query enginesThings thatcan run queriesMost RDF stores provide a SPARQL engineQuery rewritersE.g. to query relational databases (more later)EndpointsThings that accept queries on the Web and return resultsClient librariesThings that make it easy to ask queriesTypes of SPARQL Tools
- 73.Community-maintained list ofquery engineshttp://esw.w3.org/topic/SparqlImplementationsPublicly accessible SPARQL endpointshttp://esw.w3.org/topic/SparqlEndpointsMichael Bergman’s Sweet Tools searchable list:http://www.mkbergman.com/?page_id=325Finding SPARQL Tools
- 74.Editors/environmentsOiled, Protégé, Swoop,TopBraid, Ontotrack, …Developing Tools and Infrastructure
- 75.Editors/environmentsOiled, Protégé, Swoop,TopBraid, Ontotrack, …Reasoning systemsCerebra, FaCT++, Kaon2, Pellet, Racer, CEL, …Developing Tools and InfrastructurePelletKAON2CEL
- 76.Visualizing and PublishingVocabularies
- 77.Reusable, public ontologiesFOAFTheEvent OntologyMeasurement Units Ontology
- 78.Community-maintained list:http://esw.w3.org/topic/GrddlImplementationsGRDDL toolsMostGRDDL tools are adapters to existing RDF stores or SPARQL engines to allow loading or querying data from XML and XHTML sources.
- 79.What about… everythingelse?Standards don’t yet exist, but many tools exist to derive RDF and/or run SPARQL queries against other sources of data.
- 80.
- 81.Excel spreadsheetsAnzo forExcelhttp://www.cambridgesemantics.com/products/anzo_for_excel
- 82.Web-based data sourcesVirtuosoSponger Cartridgeshttp://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtSponger
- 83.
- 84.Unstructured TextZemanta WebServicehttp://developer.zemanta.com/
- 85.On the WebGoogle,Yahoo!Best BuyNY TimesUS GovernmentUK GovernmentWhere is it being used?
- 86.IndustriesOil & Gas(integration, classification)Finance (structured data, ontologies, XBRL)Publishing (metadata)Government (structured data, metadata, classification)Libraries & museums (metadata, classification)IT (rapid application development & evolution)Where is it being used?
- 87.Health CareCleveland ClinicClinicalresearchData integration, classification (= better search)UT School of HealthPublic health surveillanceSAPPHIRE—classification, ontology-driven developmentVariousClinical Decision SupportAgile, rule-driven, scalable in the face of changeWhere is it being used?
- 88.Life SciencesAgile knowledgebasesat PfizerTarget assessment at Eli LillyIntegrated information links at NovartisAstra Zeneca, J&J, UCB, …Where is it being used?CSHALS chronicles many of these uses and many more.
- 89.
- 90.These are horizontal,enabling technologies.But they apply particularly well to problems with these characteristics:Heterogeneous data from multiple sourcesIncreasing reliance on connections within this dataRapidly changing information needsSignificant early-mover advantageLarge amounts of data that would benefit from classificationWhy are Semantic Web technologies appropriate for the life sciences?Many tactical and strategic challenges in the life sciences industry feature these traits.
- 91.Getting Started withSemantic Web technologies Don’t boil the ocean.
- 92.Getting Started withSemantic Web technologies Goal: quick tactical wins on the path to large strategic valueBe sure to consider the operational ramificationsWho does what differently?Ideal Semantic Web projects/applications have an incremental path towards broad deployment that generates demonstrable value along the way
- 93.Look beyond thecore Semantic Web capabilities and consider:integration with existing enterprise systemsdevelopment & extension modelsdeployment, logging, maintenance, backuptoolinguser experienceChoose practical, enterprise-ready toolsIf you choose to build new components and assemble existing components together, it’s quite likely you’ll end up reinventing the wheel.
- 94.What level ofexpertise is necessary?Technologies only?Technologies + API?Technologies + tooling?Tooling only?…How will we acquire the expertise?In-house (and if so, how?)Vendor services3rd-party servicesOpen-source communityPlan for Acquiring Expertise
- 95.I’m always happyto field questions & engage in discussion:lee@cambridgesemantics.comThanks & Discussion
Editor's Notes
- #13 One of the goals of this tutorial is to de-mystify the all of the names of technologies, tools, projects, etc. that swirl around the Semantic Web story.And since I saw that as I researched this presentation, everyone seems to like this particular Gary Larson cartoon, it behooved me to include it.
- #18 The good – emphasize the importance of the foundational layers (URIs and RDF) ; emphasizes the long-term roadmap/vision of what’s needed for the Semantic WebThe bad – implies that perhaps things can’t be taken serious until all the pieces are in place ; implies an order to the research ; various versions of the cake tell different stories (importance of XML, absence of query, lack of UI/application layer, …)Valentin Zacharias wrote about the “infamy” part of the layer cake here: http://www.valentinzacharias.de/blog/2007/04/ban-semantic-web-layer-cake.html
- #22 The Ontology/ontology dichotomy is captured well by Jim Hendler at http://www.cs.rpi.edu/%7Ehendler/presentations/SemTech2008-2Towers.pdf
- #26 Definition.
- #27 Prescriptive.
- #28 Descriptive.
- #29 Formal.
- #32 The first is as opposed to relational tables or XML schemas where the schema needs to be explicitly adjusted to accommodate whatever data is being merged.The second is due to the expressivity of the model – can handle lists, trees, n-ary relations, etc.The third is as opposed to table & column identifiers or XML attribute names.
- #36 Definition.
- #37 Prescriptive.
- #38 Descriptive.
- #39 Descriptive (part 2). This is leagues ahead of the situation with SQL!
- #42 http://bio2rdf.org/
- #43 http://bio2rdf.org/
- #45 Definition.
- #47 Definition.
- #53 Definition.