Transcript HCLS$$ISWC2008$$Tutorial$COI

Clinical Observations
Interoperability (COI)
Helen Chen
Eric Prud‘hommeaux
Vipul Kashyap
Rachel Richesson
Jyotishman Pathak
Holger Stenzhorn
Health Care and Life Sciences
Interest Group (HCLSIG)
Motivation
• Clinical trials are conducted to collect safety
and efficacy data for new drugs or devices
• Depending on the specific trial, investigators
enroll healthy volunteers or patients
• Finding and recruiting suitable participants is
important to avoid unnecessary costs
Health Care and Life Sciences
Interest Group (HCLSIG)
Problem
• Pharmaceutical
companies have one
standard to encode
clinical trials
CDISC SDTM
• Hospitals have
another standard to
encode clinical care
HL7 DCM
• Waste of money because of two different
standards
Health Care and Life Sciences
Interest Group (HCLSIG)
Goals
• How can the gap between the two be bridged
using Semantic Web technologies?
• Map across formats
• Reuse existing data
• Develop a proof of concept application
• Demonstrate the feasibility of the approach
• Get relevant partners involved
Health Care and Life Sciences
Interest Group (HCLSIG)
Use Case Step-Through
1. (Textual) specification of the eligibility
criteria for a given clinical trial
2. Ontology-based translation of the eligibility
criteria into SPARQL queries
3. Translation of the SPARQL queries into
database-specific SQL queries
Health Care and Life Sciences
Interest Group (HCLSIG)
Use Case Step-Through
4. Execution of the queries at the database(s) –
results contain all eligible patients
5. Return of a list of eligible patients to clinical
trial administrator
Health Care and Life Sciences
Interest Group (HCLSIG)
Ontology Modeling
Health Care and Life Sciences
Interest Group (HCLSIG)
Ontology Modeling
• Develop ontologies for clinical trials and
clinical practice based on information models
CDISC SDTM and HL7 DCM
• Model all necessary patient and medication
aspects…
• Lab results and observations
• Patient vital signs
• Medications
Health Care and Life Sciences
Interest Group (HCLSIG)
Inclusion Criteria
Type 2 diabetes on diet and exercise therapy or
monotherapy with metformin, insulin
secretagogue, or alpha-glucosidase inhibitors, or
a low-dose combination of these at 50%
maximal dose. Dosing is stable for 8 weeks prior
to randomization.
…
?patient takes meformin .
Health Care and Life Sciences
Interest Group (HCLSIG)
Exclusion Criteria
Use of warfarin (Coumadin), clopidogrel
(Plavix) or other anticoagulants.
…
?patient doesNotTake anticoagulant .
Health Care and Life Sciences
Interest Group (HCLSIG)
Medication in RDF
:M0271 a sdtm:Medication;
spl:classCode 6809 ; #metformin
metformin
sdtm:subject :P0006;
sdtm:dosePerAdministration [
sdtm:hasValue 500;
sdtm:hasUnit "mg„ ];
sdtm:startDateTime
"20070101T00:00:00"^^xsd:dateTime ;
sdtm:endDateTime
"2008-0101T00:00:00"^^xsd:dateTime .
Health Care and Life Sciences
Interest Group (HCLSIG)
Criteria in SPARQL
?medication1 sdtm:subject ?patient ;
spl:activeIngredient ?ingredient1 .
metformin
?ingredient1 spl:classCode 6809 . #metformin
OPTIONAL {
?medication2 sdtm:subject ?patient ;
spl:activeIngredient ?ingredient2 .
?ingredient2 spl:classCode 11289 .
#anticoagulant
anticoagulant
} FILTER (!BOUND(?medication2))
Health Care and Life Sciences
Interest Group (HCLSIG)
Issues
1. Data is not stored only in form of the CDISC
SDTM but also in HL7 DCM form
2. Data is not stored as RDF but in conventional
relational databases
Health Care and Life Sciences
Interest Group (HCLSIG)
Solutions
1. Transform references to SDTM classes to
references to HL7 classes via N3 rules
2. Transform either…
• Relational data into RDF
• SPARQL into SQL via N3 rules
• Second approach chosen
Health Care and Life Sciences
Interest Group (HCLSIG)
SDTM to HL7 Transformation
sdtm:Medication
sdtm:dosePerAdministration
hl7:SubstanceAdministration
hl7:doseQuantity
Health Care and Life Sciences
Interest Group (HCLSIG)
{
?x a sdtm:Medication ;
sdtm:dosePerAdministration ?y
} => {
?x hl7:SubstanceAdministration ;
hl7:doseQuantity ?y
}
Behind the Scenes
• Description of the complete workflow at
http://www.w3.org/2008/Talks/
1027-ISWC/SWObjects
Health Care and Life Sciences
Interest Group (HCLSIG)