exploiting ebxml registry semantics in the ehealth domain
TRANSCRIPT
Asuman Dogac Ontolog Forum, February 9, 2006 1
Exploiting ebXML Registry Semantics in the eHealth Domain*
Asuman Dogac
* Parts of this work are being sponsored by the eHealth and eBusinessUnits of the European Commission
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Brief Introduction… ebXML registry is capable of storing semantics
about the registry objects
This semantics is restricted to classification hierarchies with properties
It is possible to represent some Web Ontology Language (OWL) constructs in the registry
Through an application in eHealth domain we will discuss how this semantics can be exploited
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Outline…
Semantics in ebXML registries
ebXML Registry Semantic Constructs
A brief introduction to OWL
Mapping OWL constructs to ebXML registry
Making ebXML registries OWL aware
Exploiting ebXML registry semantics in the
healthcare domain
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Describing Semantics in ebXML Registries ebXML registry allows metadata to be stored in the
registry
This is achieved through a classification mechanism, called ClassificationScheme
Association instances are used in relating objects in the registry
Furthermore Slot instances provide a dynamic way to add arbitrary attributes to registry object instances
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An example…
Clinical Domain
Field
SurgeryField
DermatologyField
OrganSystems
Central Nervous System
ebXML Registry
A Classification Hierarchy
ebXML Repository
ExtrinsicObject
A “NeuroSurgery" Document
LOINC
CodingSystem
classifiedBy
classifiedBy
ClassificationNodes
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ebXML Registry Implementation: Relational Database with Stored Procedures ebXML registry implementations store registry data in a relational
database
The Query Manager component constructs the objects by obtaining the required data from the relational database through SQL queries
When a client submits a request to the registry, registry objects are constructed by retrieving the related information from the database through SQL queries and are served to the user through the methods of these objects
Alternatively, SQL can be directly used to retrieve data (You need to know the relational schema)
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ebXML Registry Semantic Support Summary (I) Through the constructs provided in an ebXML
registry, it is possible to define: Classes and class hierarchies Properties through “slot” mechanism Properties of classes through predefined
association types Predefined associations can be extended Group registry objects
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ebXML Registry Semantic Support Summary (II) All this information is stored in the registry,
and
Can be used to relate registry items with one another
Can OWL ontologies be stored in ebXML registries through ebXML registry constructs?
We will give it a try!
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ebXML Registry Semantic Constructs: References ebXML, http://www.ebxml.org/ ebXML Registry Information Model v2.5,
http://www.oasis-open.org/committees/regrep/ documents/2.5/specs/ebRIM.pdf
ebXML Registry Services Specification v2.5, http://www.oasis-open.org/committees/regrep/ documents/2.5/specs/ebRIM.pdf
freebXML Registry Open Source Project, http://ebxmlrr.sourceforge.net
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Outline…
Semantics in ebXML registries
ebXML Registry Semantic Constructs
A brief introduction to OWL
Mapping OWL constructs to ebXML registry
Making ebXML registries OWL aware
Exploiting ebXML registry semantics in the
healthcare domain
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Web Ontology Language: OWL
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Ontology Languages and OWL
DAML:Darpa Agent Markup Language
OIL: Ontology Inference Layer (European
Commission Project)
DAML+OIL
OWL: Web OntologyLanguage (Being
Standardized by W3C)
RDF (ResourceDescriptionFramework)
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OWL = RDF Schema + more
All of the elements/attributes provided by RDF and RDF Schema can be used when creating an OWL document
OWL classes permit much greater expressiveness than RDF Schema classes
Consequently, OWL has created their own Class, owl:Class
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OWL Classes
Ministry of Interior has defined ontologies for their information in OWL
For example: Crimes
Robbery Speeding
<owl:Class rdf:ID=“Crimes"> </owl:Class>
<owl:Class rdf:ID=“Robbery"> <rdfs:subClassOf rdf:resource="#Crimes"/></owl:Class>
<owl:Class rdf:ID=“Speeding"> <rdfs:subClassOf rdf:resource="#Crimes"/></owl:Class>
…
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OWL Properties
<owl:DatatypeProperty rdf:ID=“description"> <rdfs:domain rdf:resource="#Crime"/> <rdfs:range rdf:resource=“http://www.w3.org/2001/XMLSchema#Literal"/>
</owl:DatatypeProperty >
<owl:ObjectProperty rdf:ID=“suspect"> <rdfs:domain rdf:resource="#Robbery"/> <rdfs:range rdf:resource=“#Thief>
</owl:ObjectProperty >
<owl:ObjectProperty rdf:ID=“driver"> <rdfs:domain rdf:resource="#Speeding"/> <rdfs:range rdf:resource=“#Speeder"/>
</owl:ObjectProperty >
suspect
Robbery Thief
Speeding Speeder
driver
Crimes Literal
description
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An Example (From Ref 3)
Finger prints from a robbery scene identified John Smith as the suspect
Here is the police report on the robbery:
<Robbery rdf:ID="report-2004-07-27-xyz"> <description>...</description> <suspect> <Thief rdf:about="http://www.ministryOfInterior.gov/criminals#John_Smith"/> </suspect>
</Robbery>
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An Example (Continued)• Later in the day a police gives a person a
ticket for speeding
• The driver's license showed the name John Doe
• Here is the police report on the speeder:
<Speeding rdf:ID="report-2004-07-27-abc"> <description>...</description> <driver> <Speeder rdf:about="http://www.ministryOfInterior/criminals#John_Doe"/> </driver>
</Speeding>
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Any Relationship between the Thief and the Speeder?
Ministry of Interior keeps the OWL descriptions of their files:
<Criminals rdf:about=" http://www.ministryOfInterior/criminals#John_Doe ">
<owl:sameAs rdf:resource=" http://www.ministryOfInterior.gov/criminals#John_Smith "/></Criminals>
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An Example OWL Reasoning (Continued)
OWL provides a property (owl:sameAs) for indicating that two resources (e.g., two people) are the same
Thief
Speeder
John Smith
John Doe
owl:sameAs
Inference: The Thief and the Speeder are one and the same!
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OWL Summary
OWL is an Ontology Specification Language It is build on RDF with DAML+OIL experience OWL has more expressive power than RDF
such as: Boolean Combinations of Class Expressions (unionOf,
intersectionOf, complementOf, …) Several Types of Properties (Transitive, Functional,
Symmetric, …) Equivalence or disjointness of classes
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OWL: References (I)
1. OWL Web Ontology Language Reference: http://www.w3.org/TR/owl-ref/
2. Costello, R. L., Jacobs, D. B., OWL Web Ontology Language, www.racai.ro/EUROLAN-2003/html/presentations/JamesHendler/owl/OWL.ppt
3. Costello, R. L., Jacobs, D. B., A Quick Introduction to OWL Web Ontology Language, www.daml.org/meetings/2003/05/SWMU/briefings/ 08_Tutorial_D.ppt
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OWL: References (II)
1. Antoniou, G., Harmalen, F., “Web Ontology Language: OWL”, in Handbook on Ontologies, Springer, 2004
2. Horrocks, I., “DAML+OIL: A Description Logic for the Semantic Web”, IEEE Data Engineering Bulletin, Vol. 25, No. 1, March 2000
3. McGuinness, D., Harmelen, F.,OWL Web Ontology Language Overview, http://www.w3.org/TR/owl-features/
4. Smith, M., Welty, C., McGuinnes, D., OWL Web Ontology Language Guide, http://www.w3.org/TR/owl-guide/
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Outline…
Semantics in ebXML registries
ebXML Registry Semantic Constructs
A brief introduction to OWL
Mapping OWL constructs to ebXML registry
Making ebXML registries OWL aware
Exploiting ebXML registry semantics in the
healthcare domain
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The Basic Ideas in Mapping OWL Constructs to ebXML Classification Hierarchies Mapping OWL classes → ebXML Classification Nodes
Mapping OWL Datatype properties → ebXML Slots
Mapping OWL Object properties → ebXML Association Types
Mapping the relationships between properties (such as “rdfs:subPropertyOf”) → Associations between associations Using existing Association Types when available
E.g. “owl:equivalentClass” → ebXML Predefined Association Type “EquivalentTo”
Creating new Association Types when necessary
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OWL Classes and RDF Properties → ebXML RIM
OWL:
<owl:Class rdf:ID=“Dermatology"> <rdfs:subClassOf rdf:resource="# ClinicalDomain"/></owl:Class>
<owl:Class rdf:ID=“DermatologyField"> <rdfs:subClassOf rdf:resource="#ClinicalDomain"/></owl:Class>
<owl:ObjectProperty rdf:ID=“equivalentTo"> <rdfs:domain rdf:resource="#Dermatology"/> <rdfs:range rdf:resource="# DermatologyField"/></owl:ObjectProperty>
Dermatology
Dermatology Field
ObjectProperty: equivalentTo
OWL classes → ebXML ClassificationNodes OWL properties → ebXML new Association TypesExample:
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OWL Classes and RDF Properties → ebXML RIM OWL classes → ClassificationNodes
OWL Properties → ebXML new Associations Types Example:
ebXML RIM:<rim:ClassificationNode id = ‘Dermatology‘ parent= 'ClinicalDomain'> <rim:Name> <rim:LocalizedString value = “Dermatology "/> </rim:Name></rim:ClassificationNode>
<rim:ClassificationNode id = ' Dermatology Field‘ parent= ‘ClinicalDomain'> <rim:Name> <rim:LocalizedString value = “Dermatology Field "/> </rim:Name></rim:ClassificationNode>
<rim:Association id = 'promotion‘ associationType = ‘ObjectProperty' sourceObject = 'Dermatology ' targetObject = ‘Dermatology Field' ><rim:Name> <rim:LocalizedString value = “equivalentTo"/> </rim:Name></rim:Association>
Clinical Domain
Dermatology Field
Dermatology
Association of type “ObjectProperty”: equivalentTo
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Summary - Mapping OWL constructs to ebXML registry (I) OWL constructs can be mapped ebXML Registry
semantic constructs
Ontologies can play two major roles in ebXML registry:
One is to provide a source of shared and precisely defined terms which can be used to dynamically discover objects in the registry
The other is to reason about the ontologies
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Summary - Mapping OWL constructs to ebXML registry (II) When an ontology language like OWL is
mapped to a class hierarchy like the one in ebXML, the first role can directly be achieved
However, for the second role, the reasoners can not directly run on the ebXML class hierarchy
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Summary - Mapping OWL constructs to ebXML registry (III) Some OWL constructs are for reasoners to use them
The fact is that we do not have industrial strength reasoners yet!
Semantic can also be taken advantage of through querying
This work is realized within the scope of IST 2104 SATINE project supported by the European Commission and details are available at: Dogac, A., Kabak, Y., Laleci, G., “Enriching ebXML Registries
with OWL Ontologies for Efficient Service Discovery”, in Proc. of RIDE'04, Boston, March 2004, http://www.srdc.metu.edu.tr/webpage/publications/
IST 2104 SATINE project http://www.srdc.metu.edu.tr/webpage/projects/satine/
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Outline…
Semantics in ebXML registries
ebXML Registry Semantic Constructs
A brief introduction to OWL
Mapping OWL constructs to ebXML registry
Making ebXML registries OWL aware
Exploiting ebXML registry semantics in the
healthcare domain
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Making ebXML registries OWL aware As already demonstrated OWL constructs
can be mapped to ebXML registry information model constructs
In this process, the ebXML Registry architecture is not modified
In this way, the semantic explicitly stored in the registry can be retrieved through querying
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Making ebXML registries OWL aware For example, “subClassOf” association is defined in
ebXML registry to express “multiple inheritance”
Yet to make any use of this semantics, the user must code the query, say, to find out all the super classes of a given class
An improvement: The code to process the OWL semantics can be stored in ebXML registry architecture through predefined procedures
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The following generic stored procedure can be used whenever necessary!
… …
SurgeryField
Central Nervous System
NeuroSurgery
CREATE PROCEDURE findSuperClasses($className) ASBEGINSELECT C2.idFROM Association A, Name_ N, ClassificationNode C1, ClassificationNode C2WHERE A.associationType LIKE 'subClassOf' AND C1.id = N.parent AND N.value LIKE $className AND A.sourceObject = C1.id AND A.targetObject = C2.idEND;
ClassificationNode(…, id, objectType, code, parent, path)Association(…, id, objectType, associationType, sourceObject, targetObject, isConfirmedBySourceOwner, isConfirmedByTargetOwner)Name_(charset, lang, value, parent)
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The following generic stored procedure can be used to find the object properties of a given class
CREATE PROCEDURE findObjectProperties($className) ASBEGINSELECT A.idFROM Association A, Name_ N, ClassificationNode CWHERE A.associationType LIKE 'objectProperty' AND C.id = N.parent AND N.value LIKE $className AND A.sourceObject = C.idEND;
By using such stored procedures some of the OWL semantics can be extracted from the ebXML registry!
ClassificationNode(…, id, objectType, code, parent, path)Association(…, id, objectType, associationType, sourceObject, targetObject, isConfirmedBySourceOwner, isConfirmedByTargetOwner)Name_(charset, lang, value, parent)
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Making ebXML registries OWL aware How about reasoning?
Reasoning entails the derivation of new data that is not directly stored in the registry
To deduce this data, rules need to be stored in the registry
However, this approach requires considerable changes in the registry architecture and brings about the efficiency considerations of rule based systems
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Making ebXML registries OWL aware: Summary After mapping OWL constructs to ebXML Registry, the
Registry can be enhanced with stored procedures to support the processing required by the OWL constructs
This work is realized within the scope of IST 2104 SATINE project supported by the European Commission and details are available at:
A. Dogac, Y. Kabak, G. B. Laleci, C. Mattocks, F. Najmi, J. Pollock, "Enhancing ebXML Registries to Make them OWL Aware", Distributed and Parallel Databases Journal, Springer, Vol. 18, No. 1, July 2005, pp. 9-36. (Science Citation Index Expanded, Impact Factor: 00.897). http://www.srdc.metu.edu.tr/webpage/publications/
IST 2104 SATINE project http://www.srdc.metu.edu.tr/webpage/projects/satine/
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Outline…
Semantics in ebXML registries
ebXML Registry Semantic Constructs
A brief introduction to OWL
Mapping OWL constructs to ebXML registry
Making ebXML registries OWL aware
Exploiting ebXML registry semantics in the
healthcare domain
Asuman Dogac Ontolog Forum, February 9, 2006 38
A Brief Introduction to Integrating Healthcare Enterprise (IHE)– Cross Enterprise Document Sharing (XDS)
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IHE - XDS
In the IHE XDS Profile, healthcare enterprises that agree to work together for clinical document sharing form an “XDS Affinity Domain“
Such institutes agree on a common set of policies such as how the patients are identified, the access is controlled, and the common set of coding terms to represent the metadata of the documents
In IHE XDS, the ebXML repository is used for storing the clinical documents in a persistent manner
The metadata stored at the ebXML registry is used to facilitate the discovery of the documents
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An IHE XDS Affinity Domain
Document Repository
ebXML Registry
DocumentSource
DocumentConsumer
1. Provide &Register
2. Register
3. Query
4. Retrieve
An XDS AffinityDomain
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Exchanging Documents between different XDS Domains However since patients expect their records to
follow them as they move from one XDS affinity domain to another, there is a need for the clinical affinity domains to be federated, that is, they should be able to exchange information
Main difficulties in doing this: Different Coding terms can be used in different XDS
domains… Different Patient identifiers may be used… …
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IHE XDS Metadata
XDS specifies a set of predefined metadata elements to be associated with XDS documents, submission sets and folders to facilitate their discovery
Some of the metadata elements are straightforward document properties such as “authorDepartment" or “creationTime”
Healthcare domain specific semantics is provided only through “classCode”s
A “classCode” is represented as an External Classification in ebXML registry
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Example Metadata Representations in ebXMLXSD Document Attribute
Definition ebRIM Representation
authorDepartment Department of the document author
Slot
practiceSettingCode The code specifying the clinical specialty where the act that resulted in the document was performed
External Classification
parentDocument Relationship
The type of relationship that the document has with the
parentDocument (e.g. Replace, addendum, or transformation)
Association Type
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Federated XDS
Document Repository
ebXML Registry
DocumentSource
DocumentConsumer1. Provide &
Register
2. Register
3. Query
4. Retrieve
XDS AffinityDomain A
Document Repository
ebXML Registry
DocumentSource
DocumentConsumer1. Provide &
Register
2. Register
3. Query
4. Retrieve
XDS AffinityDomain B
Query and Retrieve “NeuroSurgery" Documents From XDS Domain B
“NeuroSurgery" documents are coded in UMLS
with : “CentralNervousSystem” (C1269563) and
“Surgery” (C0543467)
“NeuroSurgery" Documents are coded
in LOINC code “34797-1”
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Example Clinical Domain Ontologies
Clinical Domain
Field
SurgeryField
DermatologyField
OrganSystems
Central Nervous System
Clinical Domain
Surgery
Dermatology
Neurosurgery
Intersection Of
EquivalentClass
These OWL ontologies are stored to and queried from ebXML registries as described
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Semantic Mediation…
Document Repository
ebXML Registry
DocumentSource
DocumentConsumer1. Provide &
Register
2. Register
3. Query
4. Retrieve
XDS AffinityDomain A
Document Repository
ebXML Registry
DocumentSource
DocumentConsumer1. Provide &
Register
2. Register
3. Query
4. Retrieve
XDS AffinityDomain B
Query and Retrieve “NeuroSurgery" Documents From XDS Domain B
“NeuroSurgery" documents are coded in UMLS
with : “CentralNervousSystem” (C1269563) and
“Surgery” (C0543467)
“NeuroSurgery" Documents are coded
in LOINC code “34797-1”
OWL MappingTool
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OWL Mapping Tool (OWLmt)
Latest version of OWLmt tool is available as open source at Sourceforge repository under Mozilla Public Licence. (http://sourceforge.net/projects/owlmt)
You can download source code of OWLmt tool by using a CVS client with the following parameters:
Server: cvs.sourceforge.net Repository Folder: /cvsroot/owlmt Protocol: pserver Username: anonymous Module Name: OWLmt
Veli Bicer at [email protected] can be contacted for further info on OWLmt
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Summary: Using ebXML Registry Semantics in the Healthcare Domain ebXML registry semantics support mechanisms can
be very useful
Here, a case related with IHE XDS is presented
This work is achieved within the scope of the IST 2103 Artemis project and the details are available at: Dogac, A., Laleci, G., Aden, T., Eichelberg M.,
"Enhancing IHE XDS for Federated Clinical Affinity Domain Support", submitted for publication
Artemis project http://www.srdc.metu.edu.tr/webpage/projects/artemis/
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Conclusions…
ebXML Registry offers semantic constructs
It will be beneficial to use these semantic constructs to improve real world applications
An example from eHealth domain is presented
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Thank you...Questions?
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Extra Slides on ebXML Registry Information Model
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ebXML Registry Information Model (RIM)
RegistryObject
ClassificationNode Classification
RegistryPackage ExtrinsicObject Service
AssociationRegistryEntry
ClassificationScheme
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ebXML Registry Information Model (RIM) The RegistryObject class is an abstract base class used by most
classes in the model Slot instances provide a dynamic way to add arbitrary attributes to
RegistryObject instances Association instances are RegistryObject instances that are used to
define many- to-many associations between objects in the information model
ClassificationScheme instances are RegistryEntry instances that describe a structured way to classify or categorize RegistryObject instances
ClassificationNode instances are RegistryObject instances that are used to define tree structures under a ClassificationScheme
Classification instances are RegistryObject instances that are used to classify other RegistryObject instances
RegistryPackage instances are RegistryEntry instances that group logically related RegistryObject instances together
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Some of the Predefined Association Types in ebXML RegistriesRelatedTo Relates Registry Objects
HasMember Defines the members of the Registry Package
Contains Defines that Source Registry Object contains the Target Registry Object
EquivalentTo Defines that Source Registry Object is equivalent to the Target Registry Object
Extends Defines that Source Registry Object inherits from the Target Registry Object
Implements Defines that Source Registry Object implements the functionality defined by the Target Registry Object
InstanceOf Defines that Source Registry Object is an instance of the Target Registry Object
ebXML allows this list to be extended!
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Extra Slides on OWL
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RDF Schema Features used in OWL rdfs:Class rdf:Property rdfs:subClassOf rdfs:subPropertyOf rdfs:domain rdfs:range
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Defining Property Characteristics RDF Schema provides three ways to characterize a
property: range: use this to indicate the range of values for a
property. domain: use this to associate a property with a
class. subPropertyOf: use this to specialize a property
OWL documents also use rdfs:range, rdfs:domain, and rdfs:subPropertyOf
OWL has more property types that are useful in inferencing!
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OWL provides three decreasingly expressive sublanguages OWL Full is meant for users who want maximum
expressiveness with no computational guarantees It is unlikely that any reasoning software will be able to
support complete reasoning for OWL Full
OWL DL supports those users who want the maximum expressiveness while retaining computational completeness (all conclusions are guaranteed to be computable) and decidability (all computations will finish in finite time)
OWL Lite supports those users primarily needing a classification hierarchy and simple constraints
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OWL Lite Features
(In)Equality: equivalentClass equivalentProperty sameAs differentFrom AllDifferent distinctMembers
Property Characteristics: ObjectProperty DatatypeProperty inverseOf TransitiveProperty SymmetricProperty FunctionalProperty InverseFunctionalProperty
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OWL Lite Features
Property Type Restrictions: Restriction onProperty allValuesFrom someValuesFrom
Class Intersection: intersectionOf
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OWL Full Language constructs that are in addition to those of OWL Lite Class Axioms:
oneOf, dataRange disjointWith equivalentClass
(applied to class expressions)
rdfs:subClassOf(applied to class expressions)
Boolean Combinations of Class Expressions: unionOf intersectionOf complementOf
Arbitrary Cardinality: minCardinality maxCardinality cardinality
Filler Information: hasValue
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An Example to Restriction
Example:
<owl:Class rdf:ID=“TaxPreparationService">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#paymentMethod"/>
<owl:allValuesFrom rdf:resource= "#CreditCard"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>