A Semantic-Web Representation of

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22 Οκτ 2013 (πριν από 4 χρόνια και 19 μέρες)

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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

Introduction

Clinical 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

Introduction

Semantic 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 record

Joe Doe’s record

RDF Triple Store

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 Classification

Semantic Definition of Normal DBP Data

Two DBP Measurements

Automatic Classification

Semantic Definition of Normal BP

Infer that both exam1 and exam2 are within the normal range

Semantic Reasoning Example

Has 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 month

Duration (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.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsCoded.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsIntervalQuantitative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsNarrative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsOrdinal.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREStandardLabObsQuantitative.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREPatient.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/CORENotedDrug.owl

http://informatics.mayo.edu/sharp/CEM2OWL/COREModels/COREDiseaseDisorder.owl



Secondary Use:


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

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

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

http://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: CDL

OWL


Represent SHARPn normalized data using RDF


Investigate SWRL/Drools combination for phenotyping