Index

• Hospital Data
• Databases as RDF
• Translation Tools
• CONSTRUCT approach
• Transform Queries
• example SDTM Query
• example Query Transformation
• Access Control
• Transformation Pipelines
• TODO

Hospital Data

Diabetic Patient Data

• Patients
• Observations (tests)
• Prescriptions

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

Warning: vapid example:

• 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 .
 }

Triples Transformation

(Virtual) Transformation Pipe

Pipeline

  cat sdtm.rq | \
  SWtransformer -q - hl7-sdtm.rq | \
  SWtransformer -q - db-hl7.rq -s http://hospital.example/DB/ | \
  mysql -u root DiabeticPatientsDataSet --table

SDTM Patient

Taking some medication

and not taking other medication

SDTM Query

PREFIX sdtm: <http://www.sdtm.org/vocabulary#>
PREFIX spl: <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>

SELECT ?patient ?dob ?sex ?takes ?indicDate # ?indicEnd ?contra
 WHERE {
  ?patient a sdtm:Patient ;
          sdtm:middleName ?middleName ;
          sdtm:dateTimeOfBirth ?dob ;
          sdtm:sex ?sex .

  ?ip	  sdtm:subject ?patient ;
	  sdtm:standardizedMedicationName ?takes ;

	  # nothing by ingredient in sdtm/caBIG/...
#          sdtm:startDateTimeOfMedication ?indicDate ;
	  # ; sdtm:endDateTimeOfMedication ?indicEnd
	  spl:activeIngredient ?ic . ?ic spl:classCode 6809
   .
  OPTIONAL {
  ?cp	  sdtm:subject ?patient ;
	  sdtm:standardizedMedicationName ?contra ;
# 	  sdtm:startDateTimeOfMedication ?contraDate ;
	  # ; sdtm:endDateTimeOfMedication   ?contraEnd
	  spl:activeIngredient ?cc . ?cc spl:classCode 11289
   .
  }
  FILTER (!BOUND(?cp))
} LIMIT 30

SDTM data fits a pattern

as does RIM

Graph transformations

via SemWeb rules

RIM Query

PREFIX rim: <http://www.hl7.org/v3ballot/xml/infrastructure/vocabulary/vocabulary#>

SELECT ?patient ?dob ?sex ?takes ?indicDate 
WHERE
{
  ?patient a rim:Person> .
  ?patient rim:entityName ?middleName .
  ?patient rim:livingSubjectBirthTime ?dob .
  ?patient rim:administrativeGenderCodePrintName ?sex .
  ?patient rim:substanceAdministration _:admin .
      # substance administration
      _:admin a rim:SubstanceAdministration> .
      _:admin rim:consumable _:subst .
          # substance
          _:subst rim:displayName ?takes .
          _:subst rim:activeIngredient _:ingred .
              _:ingred rim:classCode 6809  .
      _:admin rim:effectiveTime _:when .
          _:when rim:start ?indicDate .
}
LIMIT 30

pushing our query

into the database

CONSTRUCT Advantages

• intuitive — "X ⊢ Y" well understood.
• testable — execute (materialize) CONSTRUCT and query results.
• sharable — rule consequents (heads) advise query federation.

Challenges

• soundness.
• completeness.
• interface — some antecedents (bodies) represent atomic constraint.

Merged Data Ideal

Many DBs contributing
to a network of data.

Query the World

Configured query services
federating and distributing
to many DB Interfaces.

Conspicuously Absent

• Node renaming - <http://cityhospital.example/dbs/patient?id=12817>.
• Rule interaction - has limited expressivity.
  transitivity must be forward-chained in the DB

Kudos

thanks to Lilly and Lincoln Labs for funding this work.