Cui Tao, PhD - Towards Semantic-Web Based Representation

8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation

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Towards Semantic-Web BasedRepresentation and Harmonization of Standard

Meta-data Models for Clinical Studies

Cui Tao, PhD, Guoqian Jiang, PhD,

Weiqi Wei, MM, Harold R. Solbrig,

and Christopher G. Chute MD, DrPHDivision of Biomedical Statistics and Informatics,

Department of Health Sciences Research,

Mayo Clinic College of Medicine, Rochester, MN

AMIA CRI Summit 2011. March 9, 2011. San Francisco, CA


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Outline

Introduction (Jiang) Domain model vs. Meta-model Use cases

Materials and Methods (Jiang) Preliminary Findings (Tao) Discussion (Tao)


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Introduction

The use of common standardizedinformation building blocks for datacapturing and reporting facilitates the

understanding and sharing of clinicalresearch information.

For instance, the National CancerInstitute (NCI) supports a broadinitiative to standardize the CommonData Elements (CDEs) used in cancerresearch data capturing and

reporting.


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NCI Cancer Data Standards Registryand Repository (caDSR)

ISO/IEC 11179metadata registrystandard for CDErepresentation.

A set of APIs andtools used tocreate, edit,control, deploy andfind the CDEs.


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HL7 Detailed Clinical Models(DCMs)

A DCM is defined as an information model ofa discrete set of precise clinical knowledgewhich can be used in a variety of contexts.

The purpose of DCMs is to provide precisesemantic consistent data and terminologyspecification that are comparable andsharable between multiple care providers,health enterprises and standards-basedHealthcare Information Technology (HIT).


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Context of Detailed Clinical Modeling

http://wiki.hl7.org/index.php?title=Detailed_Clinical_Models


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Blood Pressure

Systolic Blood Pressure

Diastolic Blood Pressure

Body Position

SiteOfMeasurement Tilt

Pulse Pressure

24 Hr Measure BP

Derived blood pressure

Korotkoff Sounds

Sate of Patent

ReferenceValueBP

BloodPressureDropCulf Size

Device

Paradox

TypeDeviceUsed

ReferenceValueTilt


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Challenges

The interactions between informationmodel and terminology are central toachieving practical data standardization

The challenges on harmonization ofmultiple information models andsophisticated terminology models are

non-trivial.There is no single unified information

model to support clinical researchneeds.


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The Web Ontology Language(OWL)

W3C standard ontology language for theSemantic Web.

OWL was developed for ontology modelingby building hierarchies of classesdescribing concepts in a domain andrelating the classes to each other usingproperties.

OWL can also represent data as instancesof OWL classes - referred to as individuals -and it provides mechanisms for reasoningwith the data and manipulating it.


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Use Case 1:OWL-based methodology for defining a Code Binding

Interface between HL7 messages and SNOMED-CT codes(Rector et al.2006)

http://www.cs.man.ac.uk/~rector/papers/krmed2006-rector-binding-ontologies-to-ehrs.pdf

OWL-based Framework


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Use Case 2: Semantic Web Technologies for

Assessing Clinical Trials Eligibility (2009)

http://hcls.deri.org/coi/demo/


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Hypothesis

Representing clinical study meta-data models like HL7 DCMs and the

ISO11179 model in a Semantic-Webbased framework would providecomputable semantics of the models,thus facilitate the model reuse, model

harmonization, and data integration.


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Objective

To represent the HL7 detailed clinicalmodels using OWL through

leveraging the ISO 11179 standard.In the process of the OWL-based

transformation, we interpret thesemantics between elements in a

DCM using the ISO 11179 standardand identify the relevant issues.


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Materials

We randomly selected 3 DCMs:Blood PressureBody HeightBody Temperature

Available descriptionAn UML diagram basic structureAn Excel spreadsheet elementsA Word document - evidences


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Methods

Review all available informationIdentify the HL7 DCM constructsDetermine the mapping specificationbetween the model constructs and

OWL constructs

Use Protg 4 to represent the HL7DCMs in OWL

Protg 4 is an OWL ontologyediting environment developed by

Stanford


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Preliminary Findings


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The mappings between model constructsHL7 DCM Construct Source Example OWL Construct ISO 11179 Model ConstructVariable UML Class Systolic blood pressure A new OWL class Data ElementDescription for variable Excel spreadsheet The maximum pressure that is

build in the aorta when the

left ventricle contracts dc:description Code for variable UML attribute 271649006 annotation property or object

property Data Element ConceptAlternative code for variable UML attribute annotation property or objectproperty Data Element ConceptDatatype attribute PQ OWL class value_domain_datatype

(attribute of Value

Domain)Example attribute 140 mmHg skos:example Data Element ExampleVocabulary Excel spreadsheet SNOMED-CT dc: source Method UML attribute Method valueset Object property link to 0-1 value

setRelationship between variables UML association Blood pressure object property Valueset UML attribute A new OWL class. The allowedvalues are all subclasses of

this class Enumerated Value DomainValue in valueset enumeration A set of OWL classes, sub class

of the Valueset class Permissible valueDescription for value in a

valueset Excel spreadsheet dc:description Code for value in valueset Excel spreadsheet Same as code for variable Value meaningUnit attribute in mmHg muo:preferredUnit value_domain_unit_of_measure

ment (attribute of ValueDomain)


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OWL RepresentationCodes to Variables

Two options:Annotation properties:

prefRelatedCode & altRelatedCodeObject properties:

link the referenced concept instandard terminology and thevariable itself

use the semantic definitions ofthe referenced concepts


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OWL RepresentationData Type

Each HL7 data type is defined as anOWL class

Object property, HL7Datatype,connects the variable class and thedata type class


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OWL RepresentationValue Set

Valueset in DCM: Enumerated value domain An OWL class value in a valueset: Permissible value Sub-class of the value set class

code for a value in a valueset: Meaning of the value Treated as code for variable


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OWL RepresentationValue Set


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OWL RepresentationUnit and Range

Measurements Unit Ontology (muo)Unified Code for Units of Measure

(ucum)

Use OWL 2.0 data type definition


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OWL RepresentationUnit and Range

:bodyHeightinCM rdf:type owl:DatatypeProperty

rdfs:label "Body Height in CM"@en ;

muo:preferredUnit ucum:cm ;rdfs:domain BodyHeight ;

rdfs:range Minimum_and_maximum_of_body_height .

DatatypeDefinition(

:Minimum_and_maximum_of_body_heightDatatypeRestriction( xsd:decimal

xsd:minInclusive "0.000"^^xsd:decimal

xsd:maxInclusive "1000.000"^^xsd:decimal ) )


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Running Example


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Conclusion and Future Work

DCM--ISO 11179 modelOWL representationFuture work:

Semantic definition of HL7 datatypes

Cardinality constraintsSystematic transformation:

include more detailed models


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Questions?

Thank you!

Cui Tao, PhD - Towards Semantic-Web Based Representation

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