RDF Access to Relational Databases

W3C Semantic Web in Health Care and Life Sciences.

Eric Prud'hommeaux, Sanitation Engineer.
URL: http://w3.org/brief/MTYw
Last modified: $Date: 2010/03/16 19:03:21 $

This work is licensed under a Creative Commons Attribution 3.0 License, with attribution to W3C.

What's RDF?

Directed-labeled graph of propositions.

subject predicate object.
use [UI]R[ILN]s for disambiguation.
Bob knows Alice .

Using Existing Data(bases)

Global names.
http://someheathprovider.example/patientVisits/C1#info
Simple, declarative sentences.
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
http://someheathprovider.example/patientVisits/C1#info
Simple, declarative sentences.
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
provider:C1 role:patient provider:P1 .
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
provider:C1 role:patient provider:P1 .
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
http://someheathprovider.example/roles#patient
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
Future-proof.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
Future-proof.
Typed values.
e.g. ISO 8601 datetimes
provider:P1 role:birthdate "1946-11-03"^^xsd:date .

Simple assertions

Bob a Person .
Person rdfs:subClassOf Mammal .
Bob a Mammal .

boring example here,
exciting for e.g. drug classification.

... about people, ...

... medicine, ...

... life sciences, ...

... in one universe.

Integrate Databases

Mesh
Pubmed
Entrez Gene
Gene Ontology
...

Perform Queries

Publish (existence of) Answers

What's in it for us?

most of the world's data
is in documents

Leverage Web architecture

modeling
coding
scripting

Scripting

java
python
perl...

Declarative

   PREFIX :study <http://cdisc.example/sdtm>
   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 }

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")
  }
SERVICE <http://hcls.deri.org/atag/data/gabab_example.html>
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }

Scientific statements

Statements about scientific statements

Uniform Protocol

HTTP protocol, marshaling consistent with HTML forms.
SPARQL URL =

Endpoint (e.g. http://example.org/sparql)
+ "named-graph-uri=" data sources (e.g. named-graph-uri=http://example.org/reviews/ebert
+ "query=" + form-url-encoded query (e.g. query=SELECT+%3Fpatient…)

http://example.org/sparql?named-graph-uri=http%3A%2F%2Fexample.orgm%2F
reviews%2Febert&query=SELECT+%3Freview_graph+WHERE+%7B%0D%0A++GRAPH+%3Frev
iew_graph+%7B%0D%0A+++++%3Freview+rev%3Arating+10+.%0D%0A++%7D%0D%0A%7D

Sacrifices

Thesis: triples of URIs promote sharing semantics.

At what cost?

Real hospital database

Observation O
on Patient P
by Doctor D.

Real Hospital Database as RDF

Observation O
on Patient P
by Doctor D.

... Sharable RDF

   PREFIX :study <http://cdisc.example/sdtm>
   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 }

Query Transformation

PREFIX db: <…>
SELECT ?o ?d
 WHERE {
   ?o db:onPatient <Bob> .
   ?o db:byDoctor ?d .
 }

PREFIX db: <…>
SELECT observations... doctors...
  FROM observations, 
   patients ON id=observations.patient ...
   WHERE patients.name = "Bob"
 }

Use existing data.

Contribute some of your own.

RDB2RDF Working Group

Use cases
Requirements
Proposal
Spec

What I want from you.

queries
data
use cases
brains

uncle sam

RDF Formats

Turtle
RDF/XML
RDFa
GRDDL
JSON
SocialStream
RDBs

Turtle Example: Blood Pressure






<encounter7> edns:patient <patient3> .

<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .

Turtle Example: Blood Pressure






<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 .

Turtle 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 .

Turtle 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

RDF/XML Example: Blood Pressure

<rdf:RDF xmlns:edns="http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#"
	 xmlns:foaf: "http://xmlns.com/foaf/0.1/" .
	 xmlns:galen: "http://www.co-ode.org/ontologies/galen#" .
	 xmlns:snomed: "http://termhost.example/SNOMED/">
<rdf:Description rdf:about="encounter7">
  <edns:patient rdf:resource="patient3"/>
  <edns:screeningBP>s20090714c</edns:screeningBP>
</rdf:Description>
<galen:Patient rdf:about="patient3" foaf:family_name="Levin" foaf:firstName="Henry">
<rdf:Description rdf:about="s20090714c">
  <dc:date xsi:dt="http://www.w3.org/2001/XMLSchemadateTime">2009-07-14T18:23</dc:date>
  <edns:systolic xsi:dt="http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#mmHg">132</edns:systolic>
  <edns:diastolic xsi:dt="http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#mmHg">86</edns:systolic>
  <edns:posture rdf:resource="http://termhost.example/SNOMED/_163035008</edns:posture> <!-- SNOMED:sitting -->
</rdf:Description>

SPARQL Example: ER 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

SPARQL Example: 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 . # SNOMED:sitting
FILTER (?posture = snomed:_163035008 || ?posture = snomed:_163035009)
} ORDER DESC BY ?date

SPARQL Example: 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

Query Federation

SELECT ?date ?systolic ?diastolic WHERE {
...
  GRAPH <ER_admission_screenings.rdf>  {
    ?sc1 edns:patient ?patient ; dc:date ?date ;
         edns:systolic ?systolic ; edns:diastolic ?diastolic .
  }
  SERVICE <http://countyHospital.example/SPARQL>  {
    ?sc2 edns:patient ?patient ; dc:date ?date ;
         edns:systolic ?systolic ; edns:diastolic ?diastolic .
  }
  SERVICE <http://countyHospital.example/SPARQL>  {
    ?patient foo:screening ?sc3 . ?sc3 foo:patient ; dc:date ?date ;
             foo:BPmeasurement ( ?systolic , ?diastolic )
  }
}

Result forms

3 types of queries:

ASK -> boolean: does the query have any results?
CONSTRUCT -> query-templated RDF graph: uses variable bindings to return new RDF triples
DESCRIBE - server's choice RDF graph

SELECT and ASK results can be returned as XML or JSON. CONSTRUCT and DESCRIBE results can be returned via any RDF serialization (e.g. RDF/XML or Turtle).

SPARQL Resources

SPARQL Frequently Asked Questions
SPARQL implementations - community maintained list of open-source and commercial SPARQL engines
Public SPARQL endpoints - community maintained list
SPARQL extensions - collection of SPARQL extensions implemented in various SPARQL engines

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 .

Collaboration

We want your help

excited group of people
real-world impact
fun scaling problems
lots of papers
perhaps good for your career

join per <http://www.w3.org/2001/sw/hcls/#Participation>.