Index

• SPARQL graph patterns
• RIF Rules
• OWL
• POWDER
• RDB2RDF

New SPARQL Query Features

MUST:

• not exists
• aggregates
• suqueries
• project

MAY (read "MIGHT"):

• more (xpath) functions
• property paths
• query federation

SPARQL Graph Patterns

SELECT ?patient ?dob
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   …
              ?substAdmin  sdtm:subject ?patient;  sdtm:medName ?takes  …
 NOT EXISTS { ?contraAdmin sdtm:subject ?patient;  sdtm:medName ?contra … }
}

SPARQL Aggregates

SELECT ?patient ?dob SUM(?substAdmin) AS ?total
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   …
              ?substAdmin  sdtm:subject ?patient;  sdtm:medName "Illudium Phosdex"  …
} GROUP BY ?patient

SPARQL Subqueries

SELECT ?patient ?dob
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   …
              ?substAdmin  sdtm:subject ?patient;  sdtm:medName ?takes  …
  SELECT ?patient
  WHERE {
              ?contraAdmin sdtm:subject ?patient;  sdtm:medName ?contra …
  } ORDER BY ?contra LIMIT 1
}

SPARQL Project Expressions

SELECT ?patient ?dob ?contraURL
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   …
              ?substAdmin  sdtm:subject ?patient;  sdtm:medName ?takes  …
  SELECT ?patient fn:concat('http://dbpedia.org/', ?contra) AS ?contraURL
  WHERE {
              ?contraAdmin sdtm:subject ?patient;  sdtm:medName ?contra …
  } ORDER BY ?contra LIMIT 1
}

SPARQL Property Paths

SELECT ?patient ?dob
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   …
              ?substAdmin  sdtm:subject ?patient;  sdtm:ingredient* [ spl:classCode ?code ] .
}

SPARQL Query Federation

SELECT ?patient ?dob
WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   .
              ?substAdmin  sdtm:subject ?patient;  sdtm:medName ?takes  .
    SERVICE <http://drugsЯus.com/> {
	      ?takes       stdm:ingredent [ spl:classCode 6809 ] .

    }
}

Other New SPARQL Features

MUST:

• SPARQL Update
• Service Description
• Graph Management Protocol
• Entailment

SPARQL Update

INSERT {
    GRAPH <http://drugsЯus.com/mmkay> {
              ?substAdmin  sdtm:medName "Illudium Phosdex" .
    }
} WHERE {
              ?patient     sdtm:sex     ?sex;      sdtm:dob     ?dob;   .
              ?substAdmin  sdtm:subject ?patient .
    SERVICE <http://drugsЯus.com/mmkay> {
	      ?takes       stdm:ingredent [ spl:classCode 6809 ] .
    }
}

Service Description

<http://drugsЯus.com/> a sd:Service ;
		       sd:language foo:Sparql10_plus_federation ;
		       sd:entailment foo:RDFS ;
		       sd:function fn:concat .

D2R Service Description

<> a d2r:Server;
    rdfs:label "D2R Server";
    d2r:baseURI <http://localhost:2020/>;
    d2r:port 2020;
    d2r:documentMetadata [
        rdfs:comment "This comment is custom document metadata.";
    ];
	d2r:vocabularyIncludeInstances true;    
    .

Graph Management Protocol

                      DROP SILENT GRAPH <request_uri>
PUT <request_uri>  =  CREATE SILENT GRAPH <request_uri>
  … RDF payload …     INSERT DATA { GRAPH <request_uri> { … RDF payload … } }

SPARQL Entailment Regimes

Two models:

Paul rdf:type Worker .        
Paul :hasFriend Andrea .      
Andrea rdf:type Employee .    
Andrea :hasFriend Caroline .  
Caroline rdf:type Manager .

Paul rdf:type Worker .	 
Paul :hasFriend Simon .	 
Simon rdf:type Employee .
Simon :hasFriend Andrea .
Andrea rdf:type Manager .

Query:

  Paul :hasFriend _:Y .
  _:Y rdf:type Employee .
  _:Y hasFriend _:Z .
  _:Z rdf:type Manager .

Inference

• SemWeb designed for inference.
• Use sparingly.
• Standards encourage semantic interoperability.

Rules

• IF (X subClassOf Y && Y subClassOf Z) THEN (X subClassOf Z).
• IF (X subClassOf Y && Y subClassOf Z) THEN (AC32E5B7C9963E).
• Pattern expressivity:
  • logical connectives: AND, OR, NOT
  • quantifiers: forall, forsome
  • restrictions: (FILTERs)
  • term construction

Rules Interchange Format (RIF)

• IF (X subClassOf Y && Y subClassOf Z) THEN (X subClassOf Z).
• IF (X subClassOf Y && Y subClassOf Z) THEN (AC32E5B7C9963E).
• XML format.

Modeling Languages

• RDFS.
• OWL.

Inferring types

• type labels classify things in your data.
  • :Fido a :dog .
• subtype creates hierarchy of these types.
  • :dog rdfs:subClassOf :mammal .
  • ⇒ :Fido a :mammal .
• subProperty does the same for predicates.
  • :Bob my:friendsWith :Sue .
  • my:freindsWith rdfs:subProperyOf foaf:knows .
  • ⇒ :Bob foaf:knows :Sue .

Inferring types

• domain/range identify the type of the subject/object of a predicate.
  • _:B123 foaf:givenName "Bob" .
  • foaf:givenName rdfs:domain foaf:Person .
  • ⇒ _:B123 a foaf:Person .
• does not "validate" …
  • :Logan airport:code "KBOS" .
  • :Logan foaf:givenName "Logan International Airport" .
• … it "learns"
  • ⇒ :Logan a foaf:Person .

OWL - inferring lots of stuff

• transitiveProperty: if A p1 B and B p1 C, then A p1 C.
  • :Bob :worksFor :Sue .
  • :Sue :worksFor :Tom .
  • ⇒ :Bob :worksFor :Tom .
• Derivations of types.
• Derivations of identity.

Introduction to OWL

(skip to new OWL)

• Type inference.
  • :Bob a :MGHcharlesStOncologist .
• Identity inference.
  • :Bob owl:sameAs :BobSmith .
• Consitency rules.
  • An :MGHcharlstStPatient
    • is an :MGHpatient.
    • has a :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or …).
    • has an MGH Charles Street consent form.

OWL consistency rules

• An :MGHcharlstStPatient
  • is an :MGHpatient.
  • has one :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or …).
  • has an MGH Charles Street consent form.
• Limited "validation" capability.
  • _:patientX :physician _:physY
    _:physY a :MGHcharlesStOncologist
  • _:patientX :physician _:physZ
    _:physZ a :MGHcharlesStOpticiaMn
  • ⇒ :MGHcharlesStOncologist is the same as :MGHcharlesStOptician
• use disjointWith to assert that the class of :MGHcharlesStOncologists has different members than the the class :MGHcharlesStOpticians
• (use differentFrom to assert that :MGHcharlesStOncologist7 is not the same as :MGHcharlesStOptician3)

OWL type inference

• onProperty
  • :fluffy :hasChild :scratcher .
  • :scratcher a :kitten .
  • ⇒ :fluffy a :cat .

OWL identity inference

• inverseFunctionalPropery
  • :Bob foaf:mbox <mailto:bobS@foo.example> .
  • :BobSmith foaf:mbox <mailto:bobS@foo.example> .
  • foaf:mbox a owl:inverseFunctionalProperty .
  • ⇒ :Bob is the same as :BobSmith
• cardinality constraints
  • :patientEncounter5 :patient :Bob .
  • :patientEncounter5 :patient :BobSmith .
  • :patient owl:maxCardinality 1 .
  • ⇒ :Bob is the same as :BobSmith

OWL expression

• An :MGHcharlstStPatient is an :MGHpatient who has one :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or …)
• Abstract syntax

  Class(a:MGHcharlstStPatient partial a:MGHpatient)
  Class(a:MGHcharlstStPatient complete 
      restriction(a:physician
          allValuesFrom(unionOf(a:MGHcharlesStOncologist a:MGHcharlesStOptician))))

• RDF syntax:

  _:MCSO rdfs:subClassOf :MGHpatient .
  _:MCSO rdfs:subClassOf _:physType .
  _:physType owl:onProperty :physician .
  _:physType owl:allValuesFrom _:list1 .
  _:list1 rdf:first :MGHcharlesStOncologist .
  _:list1 rdf:rest _:list2 .
  _:list2 rdf:first :MGHcharlesStOptician .
  _:list2 rdf:rest rdf:nil .
  _:MCSO owl:equivalentClass :MGHcharlstStPatient .

OWL restrictions

• _:physType a owl:Restriction .
• _:physType owl:onProperty :physician .
• _:physType owl:allValuesFrom :HasScalpel .

OWL restrictions

• _:physType a owl:Restriction .
• _:physType owl:onProperty :physician .
• _:physType owl:allValuesFrom _:anotherRestriction .

OWL restrictions

• _:physType a owl:Restriction .
• _:physType owl:onProperty :physician .
• _:physType owl:allValuesFrom _:anotherRestriction .
• _:anotherRestriction a owl:Restriction .
• _:anotherRestriction owl:onProperty :has .
• _:anotherRestriction owl:allValuesFrom _:KnownScalpels .

OWL 1.1

• Syntactic Sugar
• Expressivity Extensions
• Annotations
• Langage Profiles

Syntactic Suger

• Disjoint(MGHCharlesStOncologist, MGHCharlesStOrthopedist, MGHCharlesStOptometrist)
• MGHCharlesStDoctor = DisjointUnion(MGHCharlesStOncologist, ...)
• NegativeObjectPropertyAssertion(:onMeds, <Bob>, :aspirin)

Expressivity Extensions

• AutoRegulatingProcess = ObjectHasSelf(:regulates)
• :Hand ≤ ObjectMaxCardinality(5, :hasDigit, :finger)
• IrreflectiveObjectProperty(:flowsInto)
• DisjointDataProperty(:regularPrice, :salePrice)
• DescendentOf = ObjectChainProperty(:childOf)
• HasKey(:Patient mgh:PatientId)
• DatatypeRestriction(xsd:integer :maxInclusive, 18)
• my:AdultAge = DatatypeDefinition(..)
• DataComplementOf(my:AdultAge)

Annotation Properties

Describe individuals; produce no inferences.

Punning

Permit my:Patient to stand for a class or datatype AND an concept.

This coincident naming produces no inference.

OWL 1.1 Language Profiles

POWDER

• Classes of URIs identified by substring patterns.
• OWL Semantics (compatibility with OWL Class definitions).
• XML Syntax

<dr>
  <iriset>
    <includehosts>drugsЯus.com</includehosts>
    <includepathstartswith>/antidiabetic/metformin</includepathstartswith>
  </iriset>

  <descriptorset>
    <ex:code>6809</ex:code>
 </descriptorset>
</dr>

RDF Channeling Existing Data

• XML
• Relational Databases
• Spreadsheets
• NLP

XML data

<?xml version="1.0"?>
<ClinicalDocument transformation="hl7-rim-to-pomr.xslt">
  <recordTarget>
    <patientRole>
      <patientPatient>
	<name>
	  <given>Henry</given>
	  <family>Levin</family>
	</name>
	<administrativeGenderCode code="M"/>
	<birthTime value="19320924"/>
      </patientPatient>
    </patientRole>
  </recordTarget>
  <component>
    <StructuredBody>
      <Observation>
	<code displayName="Cuff blood pressure"/>
	<effectiveTime value="200004071430"/>
	<targetSiteCode displayName="Left arm"/>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <effectiveTime value="200004071530"/>
	    <value value="132" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
      </Observation>
      <Observation>
	<code displayName="Cuff blood pressure"/>
	<effectiveTime value="200004071530"/>
	<targetSiteCode displayName="Left arm"/>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <code displayName="Systolic BP"/>
	    <effectiveTime value="200004071530"/>
	    <value value="135" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <code displayName="Diastolic BP"/>
	    <effectiveTime value="200004071530"/>
	    <value value="88" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
      </Observation>
    </StructuredBody>
  </component>
</ClinicalDocument>

• Patient history
  • Name
  • Age
  • Illnesses
• Encounter details
  • Reason for visit
  • Vitals (e.g. BP)
  • Tests
  • Prescriptions
• Facility details…

Mapped to RDF

Relational data …

… as a graph.

Relational Mappings

• D2R
• Relational Views
• RDF Views

D2R

<d2r:ClassMap
   d2r:type="eb:Customer"
   d2r:sql="SELECT Tab_K_Kunde.KundenNr, Tab_K_Kunde.FullName,
        Tab_K_Kunde.Anrede, Tab_K_Kunde_Kreditkarte.CCNo
        FROM Tab_K_Kunde_Kreditkarte INNER JOIN Tab_K_Kunde ON
        Tab_K_Kunde_Kreditkarte.KundenNr = Tab_K_Kunde.KundenNr;"
   d2r:groupBy="Tab_K_Kunde.KundenNr"
   d2r:uriPattern=
       “http://example.org/customers#@@Tab_K_Kunde.KundenNr@@“>

Re-uses OWL constructs:

<d2r:ObjectPropertyBridge d2r:property="rdf:type"
   d2r:pattern="iswc:@@Persons.Position@@"/>

Configuration consumable as RDF (SPARQL-able).

Relational Views (DDL)

create iri class prd:product_iri using
  function OPLWEB.DBA.PRODUCT_URI (in id varchar)
    returns varchar,
  function OPLWEB.DBA.PRODUCT_URI_INVERSE (in id_iri varchar)
    returns varchar .

Uses hardened algorithms from SQL land.

RDF Views

   PREFIX :mydb <http://cityhospital.example/dbs>
CONSTRUCT { ?o a               study:SubjectObservation .
            ?o study:subject   ?p .
            ?o study:clinician ?d .
            ?d :foaf:name ?dName }

    WHERE { ?o mydb:patient ?p .
            ?o mydb:doctor  ?d .
            ?d mydb:name    ?dName }

Intuitive (testable) semantics.

Inputs

• Virtuoso
• Triplify
• D2R
• Metatomix
• Ultrawrap
• SWObjects