Cui Tao, PhD - Towards Semantic-Web Based Representation
Transcript of Cui Tao, PhD - Towards Semantic-Web Based Representation
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
1/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
2/26
Outline
Introduction (Jiang) Domain model vs. Meta-model Use cases
Materials and Methods (Jiang) Preliminary Findings (Tao) Discussion (Tao)
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
3/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
4/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
5/26
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).
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
6/26
Context of Detailed Clinical Modeling
http://wiki.hl7.org/index.php?title=Detailed_Clinical_Models
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
7/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
8/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
9/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
10/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
11/26
Use Case 2: Semantic Web Technologies for
Assessing Clinical Trials Eligibility (2009)
http://hcls.deri.org/coi/demo/
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
12/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
13/26
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.
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
14/26
Materials
We randomly selected 3 DCMs:Blood PressureBody HeightBody Temperature
Available descriptionAn UML diagram basic structureAn Excel spreadsheet elementsA Word document - evidences
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
15/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
16/26
Preliminary Findings
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
17/26
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)
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
18/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
19/26
OWL RepresentationData Type
Each HL7 data type is defined as anOWL class
Object property, HL7Datatype,connects the variable class and thedata type class
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
20/26
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
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
21/26
OWL RepresentationValue Set
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
22/26
OWL RepresentationUnit and Range
Measurements Unit Ontology (muo)Unified Code for Units of Measure
(ucum)
Use OWL 2.0 data type definition
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
23/26
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 ) )
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
24/26
Running Example
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
25/26
Conclusion and Future Work
DCM--ISO 11179 modelOWL representationFuture work:
Semantic definition of HL7 datatypes
Cardinality constraintsSystematic transformation:
include more detailed models
-
8/7/2019 Cui Tao, PhD - Towards Semantic-Web Based Representation
26/26
Questions?
Thank you!