RDF for Life Sciences

W3C Semantic Web in Health Care and Life Sciences.

Eric Prud'hommeaux, Sanitation Engineer.
URL: http://tinyurl.com/ybdsnme
Last modified: $Date: 2010/03/08 18:21:43 $

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 .

Simple

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

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

RDF: fabric of assertions about people, ...

... medicine, ...

... life sciences, ...

... in one universe.

Domain Examples

W3C Semantic Web Health Care and Life Sciences Interest Group;

a group of folks researching:

BioRDF – integrated neuroscience knowledge base
Linking Open Drug Data – aggregation of Web-based drug data
Clinical Observations Interoperability – patient recruitment
Scientific Discourse – building communities through networking
Terminology – SemWeb representation of existing resources
Translational Medicine Ontology – patient-centric upper level
Clinical Decision Support – rules to help doctors and nurses

Integrate Databases

Mesh
Pubmed
Entrez Gene
Gene Ontology
...

Perform Queries

Publish (existence of) Answers

Scientific Discourse ...

Scientific Discourse expresses hypotheses

Spans health care and life sciences

Scientists use this!

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 Protocol Mechanics

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

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

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 .

Clinical Observations Interoperability

Bridge relational databases to HL7/RIM.
Bridge HL7/RIM to SDTM.
Encode some clinical protocol (inclusion/exclusion criteria) in SDTM.
Use drug ontology to map drug classes to brands.
Protocol selection in SDTM translated to RIM, relational query.
Compare this SemWeb-y approach to other approaches.

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 :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"
 }

A course view of DBpedia

A course view of LODD

Linking Open Drug Data

Inference

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

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

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 .

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>.