Semantic Web Technologies as a Framework for Clinical Informatics

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Chimezie Ogbuji

Saúde e medicina Educação

Me ,[object Object],[object Object],[object Object],[object Object]

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]

What is Informatics? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Bioinformatics ,[object Object],[object Object]

Medical Informatics ,[object Object],[object Object]

Cohort Studies ,[object Object],[object Object],[object Object],[object Object]

Retrospective Cohort Studies ,[object Object],[object Object],[object Object],[object Object]

Reasoning Methods in Biomedical Informatics

Areas of Applied Ontology ,[object Object],[object Object],[object Object],[object Object]

Challenges in Traditional C ohort Identification ,[object Object],[object Object],[object Object],[object Object]

Patient Records ,[object Object],[object Object]

Patient Records Cont. ,[object Object],[object Object]

RDF Datasets Cont. ,[object Object],[object Object]

SPARQL &Cohort Identification ,[object Object],[object Object],[object Object],[object Object]

Use of Named Graphs ,[object Object],[object Object],[object Object]

Use of Named Graphs Cont. ,[object Object],[object Object]

Patient Record Ontology ,[object Object],[object Object],[object Object],[object Object]

Integration with Cyc KB ,[object Object],[object Object],[object Object]

Semantic Research Assistant ,[object Object],[object Object],[object Object],[object Object]

“ Semantic Interface” ,[object Object],[object Object],[object Object]

CycL Query (thereExists ?ID (thereExists ?PATIENT (and (cCFhasLeftAtriumDiameter ?CATH-OR-ECHO ?DISTANCE) (patientTreated ?CATH-OR-ECHO ?PATIENT) (cCFCCFID ?PATIENT ?ID) (isa ?CATH-OR-ECHO Echocardiogram) (patientTreated ?CATH-OR-ECHO ?PATIENT) (or (and (patientSex ?PATIENT MaleHuman) (greaterThan ?DISTANCE ( (Centi Meter) 4.2))) (and (patientSex ?PATIENT FemaleHuman) (greaterThan ?DISTANCE ( (Centi Meter) 3.8)))) (temporallyBetween-Inclusive ?CATH-OR-ECHO (MonthFn January (YearFn 2008)) (DayFn 15 (MonthFn March (YearFn 2008)))))))

$SPARQL Queries SELECT ?VAR0 ?VAR1 ?VAR2 ?VAR3 ?VAR4 ?VAR5 ?VAR6 WHERE { ?VAR0 ptrec:hasSex ptrec:Sex_female . ?VAR0 a ptrec:Patient . ?VAR1 dnode:contains ?VAR0 . ?VAR1 a ptrec:PatientRecord . ?VAR1 dnode:contains ?VAR2 . ?VAR2 a ptrec:Event_evaluation_echocardiogram> . ?VAR2 ptrec:hasLeftAtriumDiameter ?VAR3 . FILTER (?VAR3 > xsd:float(3.8)) ?VAR2 dnode:contains ?VAR4 . ?VAR4 a ptrec:EventStartDate . ?VAR4 ptrec:hasDateTimeMax ?VAR5 . FILTER (?VAR5 > xsd:dateTime("2007-12-31T23:59:59")) FILTER (xsd:dateTime("2008-03-16T00:00:00") > ?VAR5) ?VAR0 ptrec:hasCCFID ?VAR6 . }$

Challenges ,[object Object],[object Object],[object Object],[object Object]

Challenges Cont. ,[object Object],[object Object],[object Object],[object Object]

Questions? ,[object Object],[object Object],[object Object]

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Some common needs for the patient registries, Electronic Health Record (EHR) systems, and clinical research repositories of the future are: semantic interoperability, adoption of standardized clinical terminology, adhoc and distributed querying interfaces, and integration with extant databases and web-based systems. A suite of standards has recently emerged from the consortium responsible for the development and oversight of the protocols of the World-wide Web (WWW). They were conceived to address data integration challenges associated with internet and intranet applications. Many of these standards and technologies are capable of addressing the challenges common to health information systems. In this talk, an introductory overview of these technologies, how they address these challenges, and a brief discussion of projects where they have been used is given.

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Semantic Web Technologies as a Framework for Clinical Informatics

1. Semantic Web Technologies as a Framework for Clinical Informatics Chimezie Ogbuji (CCF) Chris Pierce (CCF) Chris Deaton (Cycorp) Semantic Technology Conference 16 June 2009

9. Reasoning Methods in Biomedical Informatics

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21. Ontology: Diagnoses

22. Ontology: Coronary Anatomy

23. Ontology: Pathogens

24. Ontologies: Family History

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37. CycL Query (thereExists ?ID (thereExists ?PATIENT (and (cCFhasLeftAtriumDiameter ?CATH-OR-ECHO ?DISTANCE) (patientTreated ?CATH-OR-ECHO ?PATIENT) (cCFCCFID ?PATIENT ?ID) (isa ?CATH-OR-ECHO Echocardiogram) (patientTreated ?CATH-OR-ECHO ?PATIENT) (or (and (patientSex ?PATIENT MaleHuman) (greaterThan ?DISTANCE ( (Centi Meter) 4.2))) (and (patientSex ?PATIENT FemaleHuman) (greaterThan ?DISTANCE ( (Centi Meter) 3.8)))) (temporallyBetween-Inclusive ?CATH-OR-ECHO (MonthFn January (YearFn 2008)) (DayFn 15 (MonthFn March (YearFn 2008)))))))

38. SPARQL Queries SELECT ?VAR0 ?VAR1 ?VAR2 ?VAR3 ?VAR4 ?VAR5 ?VAR6 WHERE { ?VAR0 ptrec:hasSex ptrec:Sex_female . ?VAR0 a ptrec:Patient . ?VAR1 dnode:contains ?VAR0 . ?VAR1 a ptrec:PatientRecord . ?VAR1 dnode:contains ?VAR2 . ?VAR2 a ptrec:Event_evaluation_echocardiogram> . ?VAR2 ptrec:hasLeftAtriumDiameter ?VAR3 . FILTER (?VAR3 > xsd:float(3.8)) ?VAR2 dnode:contains ?VAR4 . ?VAR4 a ptrec:EventStartDate . ?VAR4 ptrec:hasDateTimeMax ?VAR5 . FILTER (?VAR5 > xsd:dateTime("2007-12-31T23:59:59")) FILTER (xsd:dateTime("2008-03-16T00:00:00") > ?VAR5) ?VAR0 ptrec:hasCCFID ?VAR6 . }

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Notas do Editor

This is a usecase exploring the use of SW technologies for managing and identifying patient populations
CWRU research is regarding efficient RDF querying and applications of clinical ontologies
Drag & Drop “DISTANCE” onto QUANTITY to connect the meaurement to the Left Atrium Diameter. Do the same for both, male & female.
Click on the blue ball in the upper left hand corner of each box containing the male & female data and drag them into the Group Box
Right click on the blue ball in the upper left-hand corner of the Group Box and change group type to “Either of the following is true.”

Semantic Web Technologies as a Framework for Clinical Informatics

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