The Semantic Web - This time... its Personal
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The Semantic Web - This time... its Personal

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My presentation on SADI, SHARE, CardioSHARE, and the new iConsent project. Presented to the faculty and students at Stanford Medical Informatics, Palo Alto, USA. May 14th, 2010. ...

My presentation on SADI, SHARE, CardioSHARE, and the new iConsent project. Presented to the faculty and students at Stanford Medical Informatics, Palo Alto, USA. May 14th, 2010.

How do we make the semantic web, and medical research, more personal? (both for the researcher and for the patient) I present some ideas we're exploring

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The Semantic Web - This time... its Personal The Semantic Web - This time... its Personal Presentation Transcript

  • Carole Goble
    “Shopping for data should be as easy as shopping for shoes!!”
  • The Semantic Web
    This time… it’s personal!
    Mark Wilkinson, PI Bioinformatics, Heart + Lung Institute @ St. Paul’s Hospital
    Vancouver, BC, Canada
  • My Lab
  • Engineering
    &
    Research
  • Programmers
    &
    Students
  • Coolness!
    &
    Study of Coolness!
  • Middleware
  • Robert Stevens
  • Shouldn’t beseen!
  • DEMO...to give you incentive to listen to the rest of the presentation
  • Show me patients with elevated creatinine along with their latest BUN and creatinine levels
    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 ?creat
    FROM <http://sadiframework.org/ontologies/patients.rdf>
    WHERE {
    ?patient rdf:typepatients:ElevatedCreatininePatient .
    ?patient pred:latestBUN ?bun .
    ?patient pred:latestCreatinine ?creat .
    }
  • VOILA!
  • There was no database...
  • There was no warehouse...
  • There was no patient data anywhere annotated as “Elevated Creatinine Patient”
  • How did I answer a question where the required data didn’t exist?
    (...no, I didn’t just make it up LOL!)
  • In the beginning was the problem...
  • The Problem
  • The Problem
  • The Holy Grail:(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.
  • The Problem
  • The Problem
  • The Solution??
  • Why not?
    Heart
    Heart
  • You don’t know what I know!
  • You don’t thinkhow I think!
  • No Personalization!
  • So… what can we do?
  • What we need
  • How do we make Bruce’s knowledge machine-readable?
  • Ontologies!
  • Two Problems with that…
  • #1 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.
    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
  • #1 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.
  • #1 Ontology Spectrum
    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.
  • #1 Ontology Spectrum
    Because it fulfils XYZ
    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.
    BecauseI say so!
  • Because I say so?!?That’s not very... Personal...
  • No room for disagreement
  • No place for scientific discourse
  • It is what it is...Because I say so!
  • Clay Shirky“Ontology is over-rated”http://www.shirky.com/writings/ontology_overrated.html
  • If we’re going to personalize the Semantic WebWe must change the way we create and use classification systems(“shelves”)
  • “Get rid of the shelf”- Clay Shirkey
  • You don’t know what I know!
  • So don’t tell MEhow data should be interpreted!
  • How do we get rid of the shelf?
  • This is going to hurt...
  • Web Servicesvs.Semantic Web
  • Web Servicesare not “connected” to the Semantic WebWhy?
  • Web ServicesXML + XML SchemaSemantic WebRDF + OWL
  • Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML
  • Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics
  • Web Services&Semantic WebFundamentally and deeply different Web technologies!
  • >1000 X more data!
  • Accessing these databases and analytical algorithms “transparently”, based on an individual researcher’s
    ideas, beliefs, and preferenceswill help us personalize medical research
  • Mark Butler (2003) Is the semantic web hype? Hewlett Packard laboratories presentation at MMU, 2003-03-12
  • Semantic Web?(my definition)
    An information system where machines can receive information from one source,re-interpret it, and correctly use itfor a purpose that the source had not anticipated.
  • Re-interpretation
    Correct re-use
    Both are critical to the personalization of research
  • Building a personalized Semantic Web…
    Step-by-step…
  • Semantic Automated Discovery and Integrationhttp://sadiframework.org(open source)
    MicrosoftResearch
    Founding partner
  • “best-practices” for Semantic Web Service provision
  • standards-compliant
  • Lightweight(only 2 “rules”)
  • Rules come from observations:
  • SADI Observation #1:
    Web Services in Bioinformatics create implicitbiologicalrelationships between their input and output
  • SADI Observation #1:
  • SADI Best Practice #1
    Make the implicit explicit…
    A Web Service should create “triples” linking the input data to the output data, thus explicitly describing the semantic relationship between them
  • SADI Best Practice #1
    This is what bioinformatics Web Services implicitly do anyway! Easy to implement this as a best-practice
  • SADI Observation #2:HTTP GET and POST
    GET guarantees the response relates to the request URI in a very precise and predictable way
    POST does not…
  • SADI Observation #2:GET and POST
    That’s why Web Services have a fundamentally different behaviour than the Semantic Web
  • SADI Observation #2:GET and POST
    We can fix that!
    (without breaking any existing rules or standards!)
  • SADI Best Practice #2
    SUBJECT URI of the output graph (triples)
    is the sameas the SUBJECT URI of the input graph (triples)
    (the output is “about” the input... Now explicitly!)
  • Consequence
    The “Semantics” of our interaction with the Web Service are now explicitandidentical to the “Semantics” of GET
  • SADI Web Service Interfaces
    Service Interfaces defined by two OWL classes:
  • SADI Web Service Interfaces
    OWL Class #1: My Input Class
  • SADI Web Service Interfaces
    OWL Class #2: My Output Class
  • SADI Web Service Interfaces
    My Service consumes OWL Individuals of Class #1and returns OWL Individuals of Class #2
    …but the URI of those two individuals is the same!(see best practice #2)
  • How do we discover services?
    Since input and output are about the same “thing”, we can automatically determine what a service doesby comparing the Input and Output OWL classes
  • How do we discover services?
    Automatically index services in a registry based on what properties (predicates) Services add to their respective input data
  • EXAMPLE
    Input Data: BRCA1 rdf:type Gene ID
    Output Data: BRCA1 hasDNASequence AGCTTAGCCA…
    Registry Index: Service provides “hasDNASequence” property to Gene IDs
  • Now we can answer questions like
    “what is the DNA sequence of BRCA1?”
     Discover a SADI Web Service that generates the DNA Sequence property for gene identifiers
  • Okay, enough tech gobbledygookWhat will this do for ME?
  • Demo #1
  • Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output ofevery conceivable analysis
  • How do we query that database?
  • “SHARE”Semantic Health And Research EnvironmentSADI client application
  • 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 .
    }
  • Recapwhat we just saw
    A standard SPARQL query was entered into SHARE, a SADI-aware query engine
  • Recapwhat we just saw
    The query was interpreted to extract the properties being queried and these were passed to SADI for Web Service discovery
  • Recapwhat we just saw
    SADIsearched-for, found, and accessed all databases and/or analytical tools capable of generating those properties
  • 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...)
  • The Holy Grail:
    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.
  • Cool!
  • …but I’m supposed to be personalizing research…
    Let’s make this a little more personal by bringing in Ontologies
  • 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
  • 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.
  • Demo #2
    Discover instances of OWL classes
    from data that doesn’t exist…
  • Data exhibits “late binding”
  • Late binding:“purpose and meaning”
    of the data isnot determined untilthe moment it is required
  • Benefit
    of late binding
    Data is amenable to
    constant re-interpretation
    ...MY interpretation
  • How?
    DO NOT
    PRE-CLASSIFY DATA
    Just hang properties on it
  • Ontologies are in the “Frames” area of the Ontology spectrum, and therefore can leverage SADI and be “executed” as workflows
  • ???
  • Did you just say
    “execute ontologies as workflows?!”
  • Show me patients with elevated creatinine along with their latest BUN and creatinine levels
    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 ?creat
    FROM <http://sadiframework.org/ontologies/patients.rdf>
    WHERE {
    ?patient rdf:typepatients:ElevatedCreatininePatient .
    ?patient pred:latestBUN ?bun .
    ?patient pred:latestCreatinine ?creat .
    }
  • Start burrowing through the OWL class  find that we need aregression model OWL class
  • 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
  • Successful decomposition of the OWL class to discover
    the need for a LinearRegression Web Service, and so on
  • VOILA!
  • Current Research ProjectBenjamin VandervalkThere are many ways to resolve these ontologies and queries into workflowsMy student Benjamin is currently studying optimization of this query resolution strategyInteresting counterpart to DBMS query resolution because there are no indices for Web Services, and other issues (e.g. Service speed) are an important factor.
  • The Holy Grail:
    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.
  • OWL Class restrictions converted into workflows
    SPARQL queries converted into workflows
    Reasoning happening in parallel with query executionData fulfilling OWL models is discovered, or generated through running analytical tools
    SADI and CardioSHARE
  • I still don’t seehow this is“Personal”??
  • SELECT ?patient ?bun ?creat
    FROM <http://sadiframework.org/ontologies/patients.rdf>
    WHERE {
    ?patient rdf:typepatients:ElevatedCreatininePatient .
    ?patient pred:latestBUN ?bun .
    ?patient pred:latestCreatinine ?creat .
    }
  • I created a small ontologydescribing my definition ofan Elevated Creatinine Patient
  • … it was MY ontology!
  • I can re-use it
  • I can modify it as I change myworld-view
  • I can publish it for others to use
  • Others can modify it to fit THEIRworld-view
  • My personal world-view is being dynamically resolved againstglobal data and knowledge
  • …but it’s bigger than that…
  • “Elevated Creatinine Patient”
  • I made that up! It came out of my head!
  • What’s another word for a world-view that you make-up?
    Hypothesis
  • Current Research Project We believe that ontologies and hypothesesare, in some ways, the same “thing”……simply assertions about individuals that may or may not exist
  • Current Research ProjectSoroushSamadiane-Copy Clinical Outcomes investigations to determine if Outcomes hypothesescan be modeled as OWL ontologies and automatically resolved by SHARE
  • Recap
    SADI 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/generated
    Find services that generate the properties we need
  • 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.
    My Purpose!!
  • What SADI + SHARE supports
    Re-interpretation
    We constantly compare the collection of properties, gathered from third-parties worldwide, to whatever world-model (query/ontology) we wish to view it through.
    MY world model
  • What SADI + SHARE supports
    Novel re-use
    There is no way for the provider to dictate how their data should be used, or how it should be interpreted. They simply add their properties into the “data cloud” and those properties are used in whatever way is appropriate forME.
  • And all this because SADI simply requires
    that the input URI
    is the same
    as the output URI
  • Important “wins”
  • Data remains distributed
    no warehouse!
  • Data is not “exposed” as a SPARQL endpoint
    greater provider-control over computational resources
  • Semi-automated SADI service writing and deployment
    Taverna
    Semantically-guided SADI service discovery and pipelining
    SADI Plug-ins
  • Where do we go from here?
  • Consent
  • Who defines my consent?
  • IRB
    (in Canada REB)
  • Where’s MY opinionin that process?
  • New Research Project - iConsent
    I define an ontology describing the conditions under which I would allow my bio/medical data to be used
    Type of study, funding source, type of information
    Highly granular, highly detailed
    Highly PERSONAL
  • New Research Project - iConsent
    Researchers approach the database with an “instance” of their study (e.g. an instance of the OBI)
    Semantic negotiation between my ontology and their study parameters determines which aspects of my data they are allowed access to (if any)
  • New Research Project - iConsent
    For Patient:
    Personalized access to personal information
    Much more granular than current consent models
  • New Research Project - iConsent
    For Researcher:
    Access to more data from willing patients
    Automated profiling of data you weren’t allowed access to – detection of sample bias!
  • Simple and Open WINS!
    Join us!
    We have recently received funding from CANARIEto assist and train service providersin deploying their own SADISemantic Web Services
    Come join us – we’re having a lot of fun!!
    http://sadiframework.org
    http://twitter.com/sadiframework
  • Credits
    Benjamin VanderValk (SADI & CardioSHARE)
    Luke McCarthy (SADI & CardioSHARE)
    SoroushSamadian (CardioSHARE)
    Microsoft Research
    Fin
    This presentation available on SlideShare: keywords ‘sadi’, ‘wilkinson’
  • Credits
    Benjamin VanderValkMSc Student
    Bioinformatics Training Programme
    Luke McCarthy Lead Programmer, SADI
    SoroushSamadian
    PhD Student
    Bioinformatics Training Programme
  • Microsoft Research