Asuman DogacOntolog Forum, March 2, 20061 Exploiting ebXML Registry Semantics in the eHealth Domain* Asuman Dogac * Parts of this work are being sponsored

Asuman Dogac Ontolog Forum, March 2, 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

Asuman Dogac Ontolog Forum, March 2, 2006 2/50

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


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


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


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


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)


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


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!


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


Outline…







healthcare domain


Web Ontology Language: OWL


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)


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


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>

…


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


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>


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>


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>


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!


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


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


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/


Outline…







healthcare domain


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


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:


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


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


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


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/


Outline…







healthcare domain


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


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


The following generic stored procedure can be used whenever necessary!

… …

SurgeryField


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)


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)


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


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/


A Recent Development…

A new proposal for an OASIS Profile…

ebXML Registry Profile for Web Ontology

Language (OWL)

Version 1.0 Draft 2

Draft OASIS Profile, January 27, 2006

Available at:http://www.oasis-open.org/apps/org/workgroup/regrep-semantic/

download.php/16421/regrep-owl-profile-1.0-draft%202.pdf


Outline…







healthcare domain


A Brief Introduction to Integrating Healthcare Enterprise (IHE)– Cross Enterprise Document Sharing (XDS)


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


An IHE XDS Affinity Domain

Document Repository

ebXML Registry

DocumentSource

DocumentConsumer

1. Provide &Register

2. Register

3. Query

4. Retrieve

An XDS AffinityDomain


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… …


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


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


Federated XDS

Document Repository

ebXML Registry

DocumentSource

DocumentConsumer1. Provide &

Register

2. Register

3. Query

4. Retrieve

XDS AffinityDomain A

Document Repository

ebXML Registry

DocumentSource


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”


Example Clinical Domain Ontologies

Clinical Domain

Field

SurgeryField

DermatologyField

OrganSystems


Clinical Domain

Surgery

Dermatology

Neurosurgery

Intersection Of

EquivalentClass

These OWL ontologies are stored to and queried from ebXML registries as described


Semantic Mediation…

Document Repository

ebXML Registry

DocumentSource


Register

2. Register

3. Query

4. Retrieve

XDS AffinityDomain A

Document Repository

ebXML Registry

DocumentSource


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


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

Alper Okcan at [email protected] can be contacted for further info on OWLmt


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/


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


Thank you...Questions?


Extra Slides on ebXML Registry Information Model


ebXML Registry Information Model (RIM)

RegistryObject

ClassificationNode Classification

RegistryPackage ExtrinsicObject Service

AssociationRegistryEntry

ClassificationScheme


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


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!


Extra Slides on OWL


RDF Schema Features used in OWL rdfs:Class rdf:Property rdfs:subClassOf rdfs:subPropertyOf rdfs:domain rdfs:range


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!


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


OWL Lite Features

(In)Equality: equivalentClass equivalentProperty sameAs differentFrom AllDifferent distinctMembers

Property Characteristics: ObjectProperty DatatypeProperty inverseOf TransitiveProperty SymmetricProperty FunctionalProperty InverseFunctionalProperty


OWL Lite Features

Property Type Restrictions: Restriction onProperty allValuesFrom someValuesFrom

Class Intersection: intersectionOf


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


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>