What is the Semantic Web?

• Simple data model.
• Suitable for arbitrary data expression.
• Global identifiers and relations.
• Built-in linking (e.g. HTML's href).
• Ontology languages (RDFS, OWL, SKOS).

Nodes and arcs

Blood Pressure Example

<encounter7> edns:patient <patient3> .

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



      

Blood Pressure Example

<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 .
             
      

Blood Pressure Example

@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 .
             

Blood Pressure Example

@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

Named Graphs

• Provenance
• Access controls
• Fuzzy middleground

Named Graphs

SELECT ?systolic ?diastolic
 WHERE {
   GRAPH <http://cro.example/study9> {
     ?encounter edns:patient ?patient .
     ?patient foaf:family_name "Levin" ; foaf:givenName "Henry" .
     ?encounter edns:screeningBP ?bp
     ?bp edns:systolic ?systolic ; edns:diastolic ?diastolic
   }
 }

Named Graphs

SELECT ?systolic ?diastolic
 WHERE {
   GRAPH my:studies {
     ?study my:meetsStandards sdtm:DEA5 ; my:graph ?graph .
   }
   GRAPH ?graph {
     ?encounter edns:patient ?patient .
     ?patient foaf:family_name "Levin" ; foaf:givenName "Henry" .
     ?encounter edns:screeningBP ?bp
     ?bp edns:systolic ?systolic ; edns:diastolic ?diastolic
   }
 }

Groups/Sets/Classes

[Named] collections of things with similar attributes.

Groups/Sets/Classes

[Named] collections of things with similar attributes.

Groups/Sets/Classes

[Named] collections of things with similar attributes.

Logic on Classes

Hospital Data

Diabetic Patient Data

• Patients
• Observations (tests)
• Prescriptions

Databases as RDF

• Observation O
• on Patient P
• by Doctor D.

Databases as RDF

• Observation O
• on Patient P
• by Doctor D.

Databases as RDF

• Observation O
• on Patient P
• by Doctor D.

Translation Tools

• SWObjects - SPARQL CONSTRUCT.
• d2r - RDF schema and conf in RDF.
• Virtuoso - DDL.
• squirrelRDF, et al, - ???.

Construct Approach

• Observation O
• on Patient P
• who has Doctor D.

CONSTRUCT Expressivity

   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 }

Transform Queries

PREFIX db: <…>
SELECT ?O ?P ?D
 WHERE {
   ?O db:onPatient ?P .
   ?O db:byDoctor ?D .
 }

(Virtual) Transformation Pipe

Real-world mappings

Who is HCLS?

W3C Semantic Web Health Care and Life Sciences Interest Group.

90+ members from industry and academia.

1 KB (350m+ triples)

papers

• IG notes
  • Knowledgebase writeup
  • KB extension
  • SWAN
  • SIOC
• BMC Bioinformatics, AMIA, ...

Workshops

Ontology mapping code.

Current Work

• BioRDF – integrated neuroscience knowledge base
  Task lead - Kei Cheung
• Linking Open Drug Data – aggregation of Web-based drug data
  Task lead - Chris Bizer
• Clinical Observations Interoperability – patient recruitment
  Task lead - Vipul Kashyap
• Scientific Discourse – building communities through networking
  Task leads - Tim Clark, John Breslin
• Terminology – SemWeb representation of existing resources
  Task lead - John Madden
• Translational Medicine Ontology – patient-centric upper level.
  Task lead - Susie Stephens

Other Projects: Clinical Decision Support...

Query Driven

we have a couple approaches:

• data warehousing
• query manipulation/federation

HCLS KB

A Knowledgebase for Neuroscience

Built by Neurocommons and the HCLS BioRDF task force.

Precise answers to complex questions:

What proteins are associated with pyramidal neurons
AND are involved in signal transduction.

Real Query

Linking Open Drug Data

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.

Scientific Discourse

Terminology

Importing terms into Semantic Web.

• Start with pharmacological classifications in SNOMED-CT and UMLS
• Create URL identifiers for terms.
• Express term relationships (e.g. pre-coordinated terms) in OWL.
• Document process and and expressivity of schema languages.

Translational Medicine Ontology

Requires data from bench to bedside.

• vested parties (mostly from pharma)
• specific use cases
• identify data sources
• code as queries
• voila, practical ontology