A Semantic-Web Representation of Clinical Element Models Cui Tao, PhD Mayo Clinic

A Semantic-Web Representation of Clinical Element Models

Cui Tao, PhD

Mayo Clinic

Acknowledgement Christopher G. Chute, MD, DrPH Robert R. Freimuth, PhD Stanley M. Huff, MD Guoqian Jiang, PhD Thomas A. Oniki, PhD Jyotishman Pathak, PhD Craig Parker, MD Deepak Sharma Feichen Shen Sridhar D. Yadav Qian Zhu, PhD

SHARPn

Normalized EHR

EHR

Database CEM

OWL

Triple Store

XML

drools

SWRL

drools

XML Schema

Database

Schema

IntroductionClinical Element Model (CEM):

Logical models ensure semantic interoperability for: Data representation Data interpretation Data exchange within and across heterogeneous

sources and applications Represented in CEML/CDL (Constraint Definition

Language) Define syntax and grammar Not semantics

IntroductionSemantic Web

Explicit and formal semantic knowledge representation

Web Ontology Language (OWL) /Resource Description Framework (RDF): Define relationships Define classes Define constraints

Consistency checking Link to other domain terminologies Harmonize with other clinical data modeling

languages Semantic reasoning

Layer1:meta-ontology

Layer2: detailed clinical element models

Layer3:patient instances

Joe Doe’s record

Jean Doe’s recordJoe Doe’s

record

RDF Triple Store

Meta-CEM.OWL

Detailed Clinical Element Model O

ntology

Semantic Reasoning Consistency checking

Cardinality constraints Data types Property allowed domains and ranges Permissible values in value sets

Classification and reasoning

Consistency Checking

Consistency Checking

Consistency Checking

Automatic ClassificationSemantic Definition of Normal DBP Data

Two DBP Measurements

Automatic ClassificationSemantic Definition of Normal BP

Infer that both exam1 and exam2 are within the normal range

Semantic Reasoning ExampleHas two outpatient (if possible) measurements

of SBP >140 or DBP > 90 at least one month after taking anti-hypertensive drugs.

Ontology:“Labetalol 100mg” (SCT318445000) is an anti-hypertensive drug (SCT1182007).

CNTRO temporal relation reasoner:5 weeks > one monthDuration (May 1 and March 1) > one month

Implementation Status Meta Ontology

Basic category classes Properties Cardinality constraints Two OWL experts and two CEM experts have

evaluated the meta-ontology to ensure it can faithfully cover the original contents

Automatic Convertor: detailed CEM ontologies

CEM-OWL convertor

Meta-Ontology

Shared CEM Ontology

CEM Core Model Ontologies

CEM Secondary Use Ontologies

import

import

import

Download the ontologies Shared Models:

http://informatics.mayo.edu/sharp/CEM2OWL/CEM-Shared.owl

CORE Models:http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObs.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsCoded.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsIntervalQuantitative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsNarrative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsOrdinal.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsQuantitative.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREPatient.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/CORENotedDrug.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREDiseaseDisorder.owl

Secondary Use: http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseDiseaseDisorder.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseNotedDrug.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUsePatient.owlhttp://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsCoded.owl

http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsIntervalQuantitative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsNarrative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsOrdinal.owl

http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsQuantitative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/SecondaryUse/SecondaryUseStandardLabObsTiter.owl

Conclusion and Future Directions Meta-Ontology: semantically defined the basic

classes, properties, their relationships, and constraints

Convertor: CDLOWL Represent SHARPn normalized data using RDF Investigate SWRL/Drools combination for

phenotyping