outline

• semweb vision from 10k feet
• semweb techs involved (layer cake)
• standards work
• 5 mins on LeeF's tutorial
• rows in the consumer reports triple store table

semweb vision from 10k feet

• simple declarative sentences
• open world model

Extensibility Example: Blood Pressure

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg .
             

Extensibility Example: Blood Pressure

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg ;
             edns:posture snomed:_163035008 . # SNOMED:sitting

semweb vision from 10k feet

• simple declarative sentences
• open world model (don't screw your users)
• re-purposes on deployed architecture
• technology and social pressure to re-use terms
• allows latent integration
• calls for new scale of standards

semweb techs involved (layer cake)

• RDF - graph model
• RDFS - subClassOf, domain
• OWL - sameAs
• RIF - if foo then bar
• SKOS - friend broaderThan gooodFriend

semweb techs involved (layer cake)

• RDF - graph model
• RDFS - subClassOf, domain
• OWL - sameAs
• RIF - if foo then bar
• SKOS - friend broaderThan gooodFriend

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 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>

standards work

• SPARQL 1.1
  • update
  • subselects
  • aggregation
  • property paths
  • RDFS/OWL semantics
  • service description
• RDB2RDF
• RDF next steps

Mashups become queries.

SERVICE <http://uu3.org:8888/7tm_receptors>
  {
    ?iuphar  iface:family      ?family .
    ?iuphar  iface:code	       ?code .
    ?iuphar  iface:iupharName  ?iupharNm .
    ?human   iface:iuphar      ?iuphar .
    ?human   iface:geneName    "GABBR1" .
    ?human   iface:entrezGene  ?humanEntrez .
  }
SERVICE <http://dbpedia.org/sparql?default-graph-uri=http%3A%2F%2Fdbpedia.org&should-sponge=&>

  {
     _:gene  dbp:entrezgene    ?humanEntrez ;
             rdfs:label        ?label ;
    FILTER (lang(?label) = "en")
  }
GRAPH <http://hcls.deri.org/atag/data/gabab_example.html>
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }

Blood Pressure Data

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg ;
             edns:posture snomed:_163035008 . # SNOMED:sitting

Emergency Room Blood Pressure Query

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic ;
} ORDER DESC BY ?date

Clinical Study Blood Pressure Query

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic ;
           edns:posture ?posture . 
FILTER (?posture = snomed:_163035008 || ?posture = snomed:_163035009)
} ORDER DESC BY ?date

Clinical Study Blood Pressure Query

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic ?posture WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic .
  OPTIONAL {
    ?screenBP  edns:posture ?posture .
  }
} ORDER DESC BY ?date

LeeF's tutorial

LeeF's SPARQL tutorial on Semantic Universe

• comprehensive tutorial
• working examples
• useful resources

Query #2: Multiple triple patterns: property retrieval

PREFIX foaf:  <http://xmlns.com/foaf/0.1/>
SELECT *
WHERE {
    ?person foaf:name ?name .
    ?person foaf:mbox ?email .
}
        

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.

RIF: XML Syntax for Rules

<!DOCTYPE Document [
  <!ENTITY ppl  "http://example.com/people#">
  <!ENTITY cpt  "http://example.com/concepts#">
  <!ENTITY dc   "http://purl.org/dc/terms/">
  <!ENTITY rif  "http://www.w3.org/2007/rif#">
  <!ENTITY func "http://www.w3.org/2007/rif-builtin-function#">
  <!ENTITY pred "http://www.w3.org/2007/rif-builtin-predicate#">
  <!ENTITY xs   "http://www.w3.org/2001/XMLSchema#">
]>

<Document 
    xmlns="http://www.w3.org/2007/rif#"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:xs="http://www.w3.org/2001/XMLSchema#">
  <payload>
   <Group>
    <id>
      <Const type="&rif;iri">http://sample.org</Const>
    </id>
    <meta>
      <Frame>
        <object>
          <Const type="&rif;local">pd</Const>
        </object>
        <slot ordered="yes">
          <Const type="&rif;iri">&dc;publisher</Const>
          <Const type="&rif;iri">http://www.w3.org/</Const>
        </slot>
        <slot ordered="yes">
          <Const type="&rif;iri">&dc;date</Const>
          <Const type="&xs;date">2008-04-04</Const>
        </slot>
      </Frame>
    </meta>
    <sentence>
     <Forall>
       <declare><Var>item</Var></declare>
       <declare><Var>deliverydate</Var></declare>
       <declare><Var>scheduledate</Var></declare>
       <declare><Var>diffduration</Var></declare>
       <declare><Var>diffdays</Var></declare>
       <formula>
         <Implies>
           <if>
             <And>
               <formula>
                 <Atom>
                   <op><Const type="&rif;iri">&cpt;perishable</Const></op>
                   <args ordered="yes"><Var>item</Var></args>
                 </Atom>
               </formula>
               <formula>
                 <Atom>
                   <op><Const type="&rif;iri">&cpt;delivered</Const></op>
                   <args ordered="yes">
                     <Var>item</Var>
                     <Var>deliverydate</Var>
                     <Const type="&rif;iri">&ppl;John</Const>
                   </args>
                 </Atom>
               </formula>
               <formula>
                 <Atom>
                   <op><Const type="&rif;iri">&cpt;scheduled</Const></op>
                   <args ordered="yes">
                     <Var>item</Var>
                     <Var>scheduledate</Var>
                   </args>
                 </Atom>
               </formula>
               <formula>
                 <Equal>
                   <left><Var>diffduration</Var></left>
                   <right>
                     <External>
                       <content>
                         <Expr>
                           <op><Const type="&rif;iri">&func;subtract-dateTimes</Const></op>
                           <args ordered="yes">
                             <Var>deliverydate</Var>
                             <Var>scheduledate</Var>
                           </args>
                         </Expr>
                       </content>
                     </External>
                   </right>
                 </Equal>
               </formula>
               <formula>
                 <Equal>
                   <left><Var>diffdays</Var></left>
                   <right>
                     <External>
                       <content>
                         <Expr>
                           <op><Const type="&rif;iri">&func;days-from-duration</Const></op>
                           <args ordered="yes">
                             <Var>diffduration</Var>
                           </args>
                         </Expr>
                       </content>
                     </External>
                   </right>
                 </Equal>
               </formula>
               <formula>
                 <External>
                   <content>
                     <Atom>
                       <op><Const type="&rif;iri">&pred;numeric-greater-than</Const></op>
                       <args ordered="yes">
                         <Var>diffdays</Var>
                         <Const type="&xs;integer">10</Const>
                       </args>
                     </Atom>
                   </content>
                 </External>
               </formula>
             </And>
           </if>
           <then>
             <Atom>
               <op><Const type="&rif;iri">&cpt;reject</Const></op>
               <args ordered="yes">
                 <Const type="&rif;iri">&ppl;John</Const>
                 <Var>item</Var>
               </args>
             </Atom>
           </then>
         </Implies>
       </formula>
     </Forall>
    </sentence>
    <sentence>
     <Forall>
       <declare><Var>item</Var></declare>
       <formula>
         <Implies>
           <if>
             <Atom>
               <op><Const type="&rif;iri">&cpt;unsolicited</Const></op>
               <args ordered="yes"><Var>item</Var></args>
             </Atom>
           </if>
           <then>
             <Atom>
               <op><Const type="&rif;iri">&cpt;reject</Const></op>
               <args ordered="yes">
                 <Const type="&rif;iri">&ppl;Fred</Const>
                 <Var>item</Var>
               </args>
             </Atom>
           </then>
         </Implies>
       </formula>
     </Forall>
    </sentence>
   </Group>
  </payload>
 </Document>

BLD Presentation Syntax

Document(
  Prefix(ppl  <http://example.com/people#>)
  Prefix(cpt  <http://example.com/concepts#>)
  Prefix(dc   <http://purl.org/dc/terms/>)
  Prefix(rif  <http://www.w3.org/2007/rif#>)
  Prefix(func <http://www.w3.org/2007/rif-builtin-function#>)
  Prefix(pred <http://www.w3.org/2007/rif-builtin-predicate#>)
  Prefix(xs   <http://www.w3.org/2001/XMLSchema#>)
  
  (* "http://sample.org"^^rif:iri _:pd[dc:publisher -> "http://www.w3.org/"^^rif:iri
                                      dc:date -> "2008-04-04"^^xs:date] *)
  Group
  (
    Forall ?item ?deliverydate ?scheduledate ?diffduration ?diffdays (
        cpt:reject(ppl:John ?item) :-
            And(cpt:perishable(?item)
                cpt:delivered(?item ?deliverydate ppl:John)
                cpt:scheduled(?item ?scheduledate)
                ?diffduration = External(func:subtract-dateTimes(?deliverydate ?scheduledate))
                ?diffdays = External(func:days-from-duration(?diffduration))
                External(pred:numeric-greater-than(?diffdays 10)))
    )
 
    Forall ?item (
        cpt:reject(ppl:Fred ?item) :- cpt:unsolicited(?item)
    )
  )
)

Other Presentation Syntaxes

Nothing standard... room for experimentation

Prefix ppl <http://example.com/people#>
Prefix cpt  <http://example.com/concepts#>
Prefix dc   <http://purl.org/dc/terms/>
Prefix rif  <http://www.w3.org/2007/rif#>
Prefix func <http://www.w3.org/2007/rif-builtin-function#>
Prefix pred <http://www.w3.org/2007/rif-builtin-predicate#>
Prefix xs   <http://www.w3.org/2001/XMLSchema#>
  
(* lt;http://sample.org> { _:pd dc:publisher lt;http://www.w3.org/>;
                                dc:date "2008-04-04"^^xs:date] } *)
if cpt:perishable(?item) and
   cpt:delivered(?item ?deliverydate ppl:John) and
   cpt:scheduled(?item ?scheduledate) and
   func:days-from-duration(?deliverydate - ?scheduledate) > 10
then cpt:reject(ppl:John ?item).

if   cpt:unsolicited(?item)
then cpt:reject(ppl:Fred ?item).

Slippery slope to "real" rule languages.

A Family of Dialects

But...

Not all engines can implement every feature

Some features (retract and negation) are incompatible

Forward chaining, Backward chaining

So...

Core: common subset

BLD: (basic logic dialect) common subset of Prolog-style languages

PRD: (production rule dialect) common subset of Production Rule languages

Use Case: Vocabulary Mapping

        if { ?x foaf:firstName ?first;
                foaf:surname ?last }
        then
           { ?x foaf:family_name ?last;
                foaf:givenname ?first;
                foaf:name func:string-join(?first " " ?last)
           }

        if { ?x foaf:name ?name } and
           pred:contains(?name, " ")
        then
           { ?x foaf:firstName func:string-before(?name, " ");
                foaf:surname func:string-after(?name, " ")
           }

Use Case: ad hoc Reasoning

        if { ?p rdfs:range ?c.   
             ?x ?p ?y }
        then
           { ?y rdf:type ?c }
        

See OWL 2 RL in RIF

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.

Using Existing Data(bases)

Using Existing Data(bases)

Using Existing Data(bases)

Using Existing Data(bases)

Using Existing Data(bases)

Using Existing Data(bases)

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.

rows in the consumer reports triple store table

• in memory
• SQL triples table
• subject-clustered triples
• column stores
• graph indexes

Graph Indexes.

Named graph proliferation demands different indexes.

SELECT ?g1 ?label ?g2 ?topic WHERE
{
GRAPH ?g1

  {
     _:gene  dbp:entrezgene    ?humanEntrez ;
             rdfs:label        ?label ;
    FILTER (lang(?label) = "en")
  }
GRAPH ?g2
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }
}