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Ontologising the Health Level Seven (HL7) Standard 
Dr. Ratnesh Sahay 
Semantics in eHealth & Life Sciences (SeLS) 
Insight Centre for Data Analytics 
NUI Galway, Ireland 
Semantic Web Application and Tools 4 Life Science (SWAT4LS) 
Freie Universitaet Berlin 
Germany 
09th December 2014
HL7 Ontologies 
• Plug & Play Electronic Patient Records (PPEPR) 
– Funding: Enterprise Ireland 
– 2006-2009 
– 2014: PPEPR-2 
– http://www.ppepr.org/ 
– Lead by me 
• HL7 OWL 
– Supported by HL7 
– 2013 - ongoing 
– http://gforge.hl7.org/gf/project/hl7owl/ 
– Lead by Lloyd McKenzie 
2/44
Tutorial Overview 
 Background 
 Ontology 
 Healthcare Interoperability 
 Health Level Seven (HL7) Messaging Environment 
 Plug and Play Electronic Patients Records (PPEPR) 
 Aligning HL7 Ontologies 
 Context & Modularity for HL7 ontologies 
3/44
Ontology ? 
 Humans like to classify things ! 
 Galaxies, Molecules, Genomics, Education 
 The Latin term ontologia was first invented in 1613 by two German philosophers 
 Rudolf Gockel 
 Jacob Lorhard 
 In context of knowledge base systems – Tom Gruber (Siri inventor !) 
 Toward Principles for the Design of Ontologies Used for Knowledge Sharing (1993) 
 A Translation Approach to Portable Ontology Specifications (1995) 
 Ontologies are 
 „Explicit Specification of a conceptualisation.“ Tom Gruber, 1993 
 Agreed between groups with explicit semantics. OWL Semantics, W3C, 2004 
 Monotonic and make Open World Assumption (OWA). OWL Semantics, W3C, 2004 
 Good at Description of Reality and their mappings. 
4/44
Healthcare Interoperability: Background 
 1986: IEEE P1157 Medical Data Interchange (MEDIX) committee introduced the 
concept of a common healthcare data model 
 1987: HL7 Version 2 
 1995-2005: HL7 Version 3 
 MEDIX work is the core of current healthcare standards (Health Level Seven (HL7), 
openEHR, CEN 13606) 
 Health Level Seven (HL7) is the most widely deployed healthcare standard ! 
 2000 onwards: HL7 Integration platforms 
 End-to-End bidirectional interface development (Mirth, iWay, iNTERFACEWARE) 
 Very few exit for Version 3 applications 
 None provided interoperability between Version 2 and Version 3 applications 
 2004 onwards: Semantic Interoperability (Ontologies) for Healthcare 
 Projects: Artemis, RIDE, SemanticHEALTH, SAPHIRE, ACGT, W3C HCLS, etc. 
 Plug and Play Electronic Patient Record (PPEPR) started end of 2006 
 Healthcare Vision: an Unified Electronic Healthcare Records (EHRs) 
5/44
Healthcare Interoperability: Current Situation 
Emergency 
Oncology 
Radiology 
Laboratory 
N*(N-1) 
Interfaces/Alignments 
6/44
Ontological Approaches 
EHR1 EHR2 
EHR4 EHR3 
(1) current situation 
(2) local alignment = (n× (n-1)) 
EHR1 EHR2 
EHR4 EHR3 
(1) ideal situation 
(2) global alignment 
EHR1 EHR2 
EHR4 EHR3 
(1) Hybrid approach 
(2) global and local alignments 
7/44
Example Scenario 
4 
Hospital A 
(Drug Policy) 
Messages 
EHR (Hospital B) 
1 
1 
2 
2 
3 
3 
V2.6 
EHR (Hospital A) 
1 Observation Order Fulfilment Request 
2 Observation Order Fulfilment Request Acknowledgement 
3 Observation Promise Confirmation 
4 
5 
5 
4 
5 
4 Observation Order Complete (Test Results) 
EHR (General 
Practitioner) 
5 Observation Order Complete Acknowledgement 
Sean Murphy 
Sean Murphy 
Diabetic patients are treated with either Insulin 
or Avandia, but not both. 
Sean Murphy 
8/44
Health Level Seven Standard (HL7)
HL7 Messaging Environment - 1: 
Semantics to Implementation 
Semantics 
type PostalAddress alias AD specializes ANY, LIST<ADXP> { 
…… 
……}; 
UML (Information Model ) 
XMLS (Implementation Technology) 
<xs:complexType name="AD" mixed="true"> 
<xs:complexContent> 
<xs:extension base="ANY"> 
<xs:sequence> 
<xs:element name="country" type="adxp.country"/> 
…… 
</xs:complexType> 
Top Middle Bottom 
HL7 Version 2 
HL7 Version 3 
AD 
ADXP 
ST 
ED 
ANY 
LIST<ADXP> 
10/44
Health Level Seven (HL7) Messaging Environment : - 2 
Schema, Alignment, and Local Policies 
HL7 V3 
Horizontal Alignments 
Hospital Hospital 
Vertical Alignments Vertical Alignments 
HL7 V2 
< 
90 complexTypes 
50 elements/ attributes 
/> 
XSD (V2) 
Trial 
Policy 
Drug 
Policy 
Access 
Policy 
< 
90 complexTypes 
50 elements/ attributes 
/> 
XSD (V2) 
< 
90 complexTypes 
50 elements/ attributes 
/> 
XSD (V3) 
< 
90 complexTypes 
50 elements/ attributes 
/> 
XSD (V3) 
Medium size hospital with 300 – 380 beds 
40,000 – 45,000 inpatients per year 
65,000 – 70,000 outpatient per year 
1000 – 1300 HL7 XSDs 
Drug 
Policy 
Bed 
Policy 
Access 
Policy 
11/44
HL7 Messaging Environment – 3: 
Contextual/Modular Information Structure 
Hospital B 
Drug Policy (2) 
Nursing domain (5) 
HL7 RIM (4) 
(Internal Objects) 
Code set (2) 
ID Schemes (1) 
Patient (345678IE) 
(1) (2) 
(3) 
Nursing domain (5) 
ID Schemes (1) 
Patient ID (1) 
(1) 
(2) 
(3) 
 Each entity is identified by an unique Object Identifiers (OIDs) 
 Health records are arranged in separate modules 
 Constraints or Policies are identifiable local modules 
Patient ID (2) 
HL7 Internal Objects 
with Unique OIDs 
Hospital A 
Drug Policy (2) 
Code set (1) 
Patient (678970W) 
HL7 RIM (3) 
(Internal Objects) 
HL7 Internal Objects 
with Unique OIDs 
12/44
HL7 Messaging Environment – 4: 
Example 
<affectedPerson 
codeSystem="2.5.1.76.1.1"> 
<name use="L"> 
<first>Sean</first> 
<last>Murphy</last> 
</name> 
</ affectedPerson> 
<identifiedPerson 
codeSystem=" 2.5.1.44.2.1 "> 
<name use="L"> 
<given>Sean</given> 
<family>Murphy</family> 
</name> 
</identifiedPerson> 
HL7 v3 
UML 
XSD 
XML 
<PID.5> 
<XPN.3>Sean Murphy</XPN.3> 
<XPN.7>L</XPN.7> 
</PID.5> 
<PID.5> 
<XPN use=“S”> 
<XPN.1> Sean </XPN.1> 
<XPN.2> Murphy </XPN.2> 
</XPN> 
</PID.5> 
HL7 v2 
XSD 
XML 
Context Hospital A: 
Patient.hasMedication (Insulin->intersection(Avandia))=isEmpty() 
Drug 
Policy 
131/34/451
Ontologising Health Level Seven Standard (HL7)
Ontology Building Methodologies 
 Features Indentified 
 Reusability of non-ontological structured resources 
 Layering of ontologies 
 Local adaptation of ontologies 
Enterprise 
Ontology 
METHONTOLOGY On-To -Knowledge DILIGENT 
Reusability +/- +/- +/- +/- 
Layering - - - +/- 
Local Adaptation - - - + 
151/54/451
PPEPR Methodology 
Methodological 
DILIGENT 
PPEPR Methodology 
METHONTOLOGY 
Enterprise Ontology 
On-To-Knowledge 
Empirical 
Domain Experiences 
Road Maps 
161/64/451
PPEPR Methodology 
9. Testing 
3. Language Selection 
4. Development Tools 
5. Lift HL7 Resources 
7. Local Adaptation 
Modelling Technology Support 
6. Layering 
1. Indentify Purpose 
2. Indentify HL7 Resources 
Scoping 
8. Alignment 
171/74/451
Modelling: Lifting HL7 Resources 
Language Transformation: A Hard problem 
XML Schema Ontology 
Data type (1) Supports large number of data types (1) RDFS/OWL 1 has limited support, thanks to 
OWL 2 for extended data types support 
Structure (1) Nested data structure 
(2) Tree structure ( top element is root) 
(3) Sequence to describe element order 
(1) Concept composition is through properties 
(2) Graph based (Any concept could be root) 
(3) No ordering of concepts 
Relation (1) Inheritance through Type and Extension 
(2) No Support 
(1) Multiple Inheritance 
(2) Inheritance on properties and logical 
implications (symmetric, Transitive, etc.) 
181/84/451
Transformation Rules 
 MIF2OWL 
 XSD2OWL 
element|attribute attribute 
element@substitutionGroup 
element@type type 
complexType|group|attributeGroup class | containedClass 
maximumMultiplicity| 
minimumMultiplicity 
@maxOccurs 
@minOccurs 
childClass 
extension@base|restriction@base 
union@memberTypes 
attribute@classCode type=Class 
HL7 MIF 
StaticModel.association| 
StaticModel.attribute 
Annotation@appinfo 
hl7:LongName|hl7:Type 
otherAnnotation | appInfo 
OWL 
ObjectProperty|DataProperty 
SubPropertyOf 
Range 
Class 
SubClassOf 
max|min 
Annotations@label|comment 
191/94/451
Example 
<xs:simpleType name="ActClassObservation"> 
<xs:annotation> 
<xs:documentation>specDomain: S11529 (C-0-T11527-S13856-S11529-cpt)</xs:documentation> 
</xs:annotation> 
<xs:union memberTypes="ActCondition ActClinicalTrial ActSpecimenObservation ActGenomicObservation "> 
</xs:union> 
</xs:simpleType> 
<xsl:for-each select="xsd:union[@memberTypes and parent::xsd:simpleType] | 
xsd:simpleContent/xsd:union[@memberTypes and parent::xsd:simpleContent“ ] 
<xsl:if test="@memberTypes"> 
<xsl:for-each select="tokenize(@memberTypes, 's')"> 
Class: <xsl:value-of select="." /> 
SubClassOf: 
<xsl:value-of select="$currentClass"/> 
</xsl:for-each> 
Class: ActCondition SubClassOf: ActObservation 
Class: ActClinicalTrial SubClassOf: ActObservation 
Class: ActSpecimenObservation SubClassOf: ActObservation 
Class: ActGenomicObservation SubClassOf: ActObservation 
202/04/451
Example 
<xs:complexType name="Patient"> 
<xs:sequence> 
<xs:element maxOccurs="unbounded" minOccurs="1" name="id" type="II"/> 
<xs:element maxOccurs="1" minOccurs="1" name="name" type="EN"/> 
<xs:element maxOccurs="1" minOccurs="1" name="administrativeGenderCode" type="CE"/> 
<xs:element maxOccurs="1" minOccurs="1" name="birthTime" type="TS"/> 
<xs:element maxOccurs="unbounded" minOccurs="1" name="addr" type="AD"/> 
..... 
</xs:sequence> 
<xs:attribute fixed="PSN" name="classCode" type="EntityPerson" use="optional"/> 
</xs:complexType> 
Class: <xsl:value-of select="$currentClass"/> 
<xsl:for-each select="xsd:attribute[@name="classCode"] 
<xsl:if test="@name='classCode'"> 
SubClassOf: <xsl:value-of select="@type"/> 
</xsl:for-each> 
Class: Patient SubClassOf: EntityPerson 
ObjectProperty: id Domain: Person Range: II 
ObjectProperty: name Domain: Person Range: EN 
ObjectProperty: administrativeGenderCode Domain: Person Range: CE 
ObjectProperty: birthTime Domain: Person Range: TS 
ObjectProperty: addr Domain: Person Range: AD 
212/14/451
Layering of Ontologies 
Top-down Bottom-up 
× 
Local 
Ontology 
Local 
Ontology 
Global 
Ontology 
(HL7 V2) 
Global 
Ontology 
(HL7 V3) 
× 
HL7 V2 
(coreSchemas) 
HL7 V3 
(coreSchemas) (1) Datatype 
(2) Vocabulary 
(common for all hospitals) 
Message 
Ontology 
+ + 
Message 
Ontology 
Message 
Ontology 
Message 
Ontology 
HL7 V2 XSD(1) HL7 V2 XSD(2) HL7 V3 XSD(1) HL7 V3 XSD(2) 
Local Alignment 
Merging 
Message Schema 
(hospital-specific) 
Lifting 
Global Alignment 
Lifting 
22/44
Local Ontology: Merging Local Ontologies 
Class: ObservationRequest 
SubClassOf: ActObservation 
Class: SpecimenObservation 
SubClassOf: ActObservation 
Class: Observer SubClassOf: RoleClass 
Class: DiabeticType2Observation 
SubClassOf: SpecimenObservation 
Class: ObservationOrder.POOB_MT210000UV 
SubClassOf: ActObservation 
Class: Observer.POOB_MT210000UV 
SubClassOf: RoleClass 
Class: HemoglobinObservation.POOB_MT210000UV 
SubClassOf: ActObservation 
= 
= 
⊑ 
Class: ObservationRequest SubClassOf: ActObservation 
+ 
Class: SpecimenObservation SubClassOf: ActObservation 
Class: Observer SubClassOf: RoleClass 
Class: HemoglobinObservation.POOB_MT210000UV SubClassOf: ActObservation 
Class: DiabeticType2Observation SubClassOf: SpecimenObservation HemoglobinObservation.POOB_MT210000UV 
232/34/451
Aligning HL7 ontologies
Alignment: HL7 Global and Local Ontologies 
HL7 v3 
HL7 v2 
GLOBAL LOCAL 
PID 
PDI 
XAD 
XON 
PID.5 
XPN.1 
XPN.2 
Person 
Role 
Ad 
Organisation 
FirstName 
classCode 
Uni. Hospital 
Name 
LabTestOrder 
Id 
Pub. Hospital 
Name 
OBX1.2 
identification 
GLOBAL LOCAL 
First Name LabTestOrder 
25/44
Alignment: Example 
Version 3 Version 3 
Class: ObservationRequest SubClassOf: ActObservation 
Class: SpecimenObservation SubClassOf: ActObservation 
Class: Observer SubClassOf: RoleClass 
Class: DiabeticType2Observation 
SubClassOf: SpecimenObservation 
Class: ObservationOrder.POOB_MT210000UV 
SubClassOf: ActObservation 
Class: Observer.POOB_MT210000UV SubClassOf: RoleClass 
Class: HemoglobinObservation.POOB_MT210000UV 
SubClassOf: ActObservation 
Version 3 Version 2 
Class: AD 
ObjectProperty: AD.1 Domain: AD Range: AD.1.CONTENT 
ObjectProperty: AD.2 Domain: AD Range: AD.2.CONTENT 
ObjectProperty: AD.3 Domain: AD Range: AD.3.CONTENT 
Class: AD SubClassOf: ANY 
ObjectProperty: streetAddressLine Domain: AD Range: Adxp.country 
ObjectProperty: state Domain: AD Range: Adxp.state 
ObjectProperty: city Domain: AD Range: Adxp.city 
<xsd:complexType name="AD.3.CONTENT"> 
<xsd:annotation> 
<xsd:appinfo> 
<hl7:Type>ST</hl7:Type> 
<hl7:LongName>City</hl7:LongName> 
</xsd:appinfo> 
</xsd:annotation> 
HL7 Annotation 
262/64/451
Ontology Alignment Tools 
Method/Tool HL7 (V3 –V3) precision-recall 
(Local Ontologies) 
HL7 (V2-V3) precision-recall 
(Global/Local Ontologies) 
Threshold Value 
Falcon-AO 70%(p)-60%(r) 
70%(p)-50%(r) 
70%(p)-50%(r) 
30%(p)-30%(r) 
30%(p)-20%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
H-Match 80%(p)-100%(r) 
80%(p)-90%(r) 
80%(p)-90%(r) 
40%(p)-30%(r) 
40%(p)-20%(r) 
40%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
BLOOMS 90%(p)-40%(r) 
90%(p)-30%(r) 
90%(p)-30%(r) 
90%(p)-20%(r) 
90%(p)-10%(r) 
90%(p)-10%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
RiMOM 60%(p)-100%(r) 
70%(p)-90%(r) 
70%(p)-90%(r) 
40%(p)-40%(r) 
40%(p)-40%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
AgreementMaker 70%(p)-100%(r) 
70%(p)-90%(r) 
70%(p)-90%(r) 
40%(p)-50%(r) 
40%(p)-50%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
27/44
Alignment: SPARQL Recipes 
Class Matching 
CONSTRUCT { ?v3 owl:equivalentClass ?v2 } 
WHERE { ?v3 rdf:type owl:Class . ?v2 rdf:type owl:Class . 
?v2 rdfs:label ?LongName . 
{FILTER regex(str(?v3), str(?LongName), ``i'')}} 
Property Matching 
CONSTRUCT { ?v3 owl:equivalentProperty ?v2 } 
WHERE { ?v3 rdf:type owl:ObjectProperty . 
?v2 rdf:type owl:ObjectProperty . 
?v2 rdfs:range ?v2range . 
?v3 rdfs:range ?v3range . 
?v2 rdfs:domain ?v2domain . 
?v3 rdfs:domain ?v3domain . 
?v2range owl:equivalentClass ?v3range . 
?v2domain owl:equivalentClass ?v3domain }; 
28/44
Alignment: SPARQL Recipes 
Method/Tool HL7 (V3 –V3) precision–recall 
(Local Ontologies) 
HL7 (V2-V3) precision-recall 
(Global/Local Ontologies) 
Threshold Value 
Falcon-AO 70%(p)-60%(r) 
70%(p)-50%(r) 
70%(p)-50%(r) 
30%(p)-30%(r) 
30%(p)-20%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
H-Match 80%(p)-100%(r) 
80%(p)-90%(r) 
80%(p)-90%(r) 
40%(p)-30%(r) 
40%(p)-20%(r) 
40%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
BLOOMS 90%(p)-40%(r) 
90%(p)-30%(r) 
90%(p)-30%(r) 
90%(p)-20%(r) 
90%(p)-10%(r) 
90%(p)-10%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
RiMOM 60%(p)-100%(r) 
70%(p)-90%(r) 
70%(p)-90%(r) 
40%(p)-40%(r) 
40%(p)-40%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
AgreementMaker 70%(p)-100%(r) 
70%(p)-90%(r) 
70%(p)-90%(r) 
40%(p)-50%(r) 
40%(p)-50%(r) 
30%(p)-20%(r) 
0.1-0.4 
0.4-0.7 
0.7-1 
SPARQL Recipes 80%(p)-90%(r) 50%(p)-60%(r) NA 
Extend alignment tools (AgreementMaker, RiMOM) by including domain-specific 
thematic structures instead of general information structures like WordNet, 
Wikipedia, DBpedia 29/44
Context, Modularity and Local Policies
Example Scenario 
PPEPR 
Hospital Drug Policy 
Messages 
Inconsistency 
Observation Order Fulfilment Request 
Observation Order Fulfilment Request Acknowledgement 
Observation Promise Confirmation 
Observation Order Complete (Test Results) 
Class: rxnorm:Avandia 
SubClassOf: galen:Drug 
Class: rxnorm:Insulin 
SubClassOf: galen:Drug 
EquivalentProperties: 
HospitalA:hasMedication 
HospitalB:EHR (Hospital hasTreatment 
B) 
1 
1 
2 
2 
3 
3 
1 
2 
3 
4 
4 
5 
5 
4 
5 
4 
5 
EHR (Hospital A) 
EHR (General 
Practitioner) 
DisjointClasses: 
HospitalA:hasMedication some rxnorm:Avandia 
HospitalA:hasMedication some rxnorm:Insulin 
Sean HospitalA:hasMedication rxnorm:Insulin 
Sean HospitalB:hasTreatment rxnorm:Avandia 
Observation Order Complete Acknowledgement 
31/44
Where is the Fault ? 
 Ontologies are 
 „Specification of a conceptualization.“ Tom Gruber, 1993 
 Agreed between groups with explicit semantics. OWL Semantics, W3C, 2004 
 Monotonic and make Open World Assumption (OWA). OWL Semantics, W3C, 2004 
 Good at Description of Reality and their mappings. 
 Ontology are not 
 Model of local and context-specific information 
 Model of time-dependent information 
 Model of context-specific constraints (e.g., policy, preferences) and 
validation 
32/44
State-OF-The-Art -1 : Formal Approaches 
 We did investigation for support of five features 
 Context-awareness (CA) 
 Modularity (M) 
 Profile and policy management (P & PM) 
 Correspondence expressiveness (CE) 
 Robustness to heterogeneity (RH) 
Considered Approaches: 
 Standard DL: Web Ontology Language (OWL) 
 No localised or contextualised semantics 
 Reusability or knowledge integration is limited to owl:imports 
 Context-Extensions of DLs : Distributed Description Logic (DDL) 
 Packet Description Logic (PDL) 
 Integrated Distributed Description Logic (iDDL) 
 E-connection 
 DL+Constraints/Rules 
 DL+DL-Safe Rules 
 Database-Style Integrity Constraints (IC) within OWL (OWL/IC in Pellet) 
 Rule-based 
 Modular Web Rule Bases 
 Query-Based 
 Query-Translation 
NONE OF THEM ADDRESSES ALL FEATURES 
 Repairing and Reasoning with Inconsistencies (DeLP) 
33/44
State-of-the-Art-2 (RDF) 
 Resource Description Framework (RDF) 
 RDF is an assertional logic (antecedent or premises is always true), where each triple expresses a 
simple proposition. [W3C RDF Semantics document] 
– In result, triple (s p o) represent facts, notion of “universal truth”. 
– RDF triples are context-free 
 Reification 
 N statements about a statement 
 Good for making statements about provenance 
 NO coupling with the truth of the triple that has been reified 
 Cannot relate the truth of a triple in one context (graph) to another 
 Named Graphs 
 Assigned an ID (URI) to each graph 
 Good for making statements about provenance 
 Associate named graphs with triples 
– Triples become quadruples 
– Fourth element is the URI of the named graph (origin) 
 Similar to Reification for the “truth of a triple” 
 N3-Context 
 Similar to Reification as far as “truth of a triple” is concerned 
34/44
Standard Semantics : OWL 
O=〈T,A〉 {0= ontology, T=Tbox, A=Abox} 
Class: rim:RolePatient 
SubClassOf: rim:Role 
Class: HA:IrishPPSId 
THA THB 
SubClassOf: rim:EntityIdentification 
Class: HA:LabTestOrder 
SubClassOf: rim:Act 
Class: HA:HemoglobinTest 
SubClassOf: rim:Act 
Class: galen:Patient 
SubClassOf: galen:Human 
Class: HB:OrderLabObservation 
SubClassOf: galen:OrderAct 
ObjectProperty: HB:hasTreatment 
DisjointClasses: 
HA:hasMedication some rxnorm:Avandia 
HA:hasMedication some rxnorm:Insulin 
Class: rxnorm:Avandia 
SubClassOf: galen:Drug 
Class: rxnorm:Insulin 
SubClassOf: galen:Drug 
= 
= 
= 
353/54/451
Distributed Description Logic (DDL) 
Oi=〈Ti,Ai, rij〉 {0i= ontology, Ti=Tbox, Ai=Abox, rij = Bridge Rules} 
Class: rim:RolePatient 
SubClassOf: rim:Role 
Class: HA:IrishPPSId 
THA THB 
= 
SubClassOf: rim:EntityIdentification 
Class: HA:LabTestOrder 
SubClassOf: rim:Act 
Class: HA:HemoglobinTest 
SubClassOf: rim:Act 
Class: galen:Patient 
SubClassOf: galen:Human 
Class: HB:OrderLabObservation 
SubClassOf: galen:OrderAct 
ObjectProperty: HB:hasTreatment 
DisjointClasses: 
= 
HA:hasMedication some rxnorm:Avandia 
HA:hasMedication some rxnorm:Insulin 
Class: rxnorm:Avandia 
SubClassOf: galen:Drug 
Class: rxnorm:Insulin 
SubClassOf: galen:Drug 
= 
HA:( HA:hasMedication some rxnorm:Insulin ) ⊑ HB:( HB:hasTreatment some rxnorm:Insulin ) 
HA:( not HA:hasMedication some rxnorm:Avandia ) ⊑ HB:( not HB: hasTreatment some rxnorm:Avandia) 
363/64/451
Packet Description Logic (PDL) 
Oi=〈Ti,Ai〉 {0i= ontology, Ti=Tbox, Ai=Abox} 
Class: rim:RolePatient 
SubClassOf: rim:Role 
Class: HA:IrishPPSId 
THA THB 
= 
SubClassOf: rim:EntityIdentification 
Class: HA:LabTestOrder 
SubClassOf: rim:Act 
Class: HA:HemoglobinTest 
SubClassOf: rim:Act 
Class: galen:Patient 
SubClassOf: galen:Human 
Class: HB:OrderLabObservation 
SubClassOf: galen:OrderAct 
ObjectProperty: HB:hasTreatment 
DisjointClasses: 
= 
HA:hasMedication some rxnorm:Avandia 
HA:hasMedication some rxnorm:Insulin 
Class: rxnorm:Avandia 
SubClassOf: galen:Drug 
Class: rxnorm:Insulin 
SubClassOf: galen:Drug 
= 
Class: ( HA:HemoglobinTest and (rim:measures some loinc: 4545-4) ) 
EquivalentTo: ( galen:BloodSugarTest and (HB:hasCode some snomed: 43396009) ) 
373/74/451
Database Style-IC 
O=〈Tn, TC, A〉 {0= ontology, Tn =Normal Tbox,TC = Constraint Tbox, A=Abox} 
Class: rim:RolePatient 
SubClassOf: rim:Role 
Class: HA:IrishPPSId 
SubClassOf: rim:EntityIdentification 
Class: HA:LabTestOrder 
SubClassOf: rim:Act 
Class: HB:HemoglobinTest 
SubClassOf: rim:Act 
Class: galen:Patient 
SubClassOf: galen:Human 
Class: HB:OrderLabObservation 
SubClassOf: galen:OrderAct 
ObjectProperty: HB:hasTreatment 
DisjointClasses: 
HA:hasMedication some rxnorm:Avandia 
HA:hasMedication some rxnorm:Insulin 
Class: rxnorm:Avandia 
SubClassOf: galen:Drug 
Class: rxnorm:Insulin 
SubClassOf: galen:Drug 
Tn(HA) 
= 
= 
= 
Tn(HB) 
TC(HA) 
383/84/451
Feature Comparisons 
Context-awareness 
Modularity Profile & Policy 
Management 
DL/OWL - -/+ - 
DDL/C-OWL + + - 
P-DL + + - 
DDL Revisited + + - 
IDDL + + - 
E-connection + + - 
RDFS-C (Guha’s) + -/+ - 
Query-based -/+ - - 
Modular Rule bases + + -/+ 
OWL/IC - -/+ -/+ 
DeLP/Paraconsistent - - -/+ 
39/44
Envisioned Situation 
- Context & Policy aware ontological model and reasoning 
GALEN SNOMED RIM 
Global (D) 
Policy1 Policy2 Policy3 Policyn 
Local (P) 
GALEN SNOMED RIM 
Local (P) Global (D) 
Hospital A Hospital B 
Policy1 Policy2 Policy3 Policyn 
414/14/451
Summary 
 An ontology is good at the top-down modeling of a domain 
 reduces the bilateral correspondences between healthcare applications 
 delegates the majority of mediation to the central integration location 
 An ontology provides an executable (comparing to HL7 UML model) semantics 
and consistent model 
 The Semantic Web layer cake allows to engage information model, schema, and 
instances under a single framework. In HL7 they are represented in three 
isolated layers. 
 An automated ontology alignment is a great support for the domain experts 
comparing manual syntactic alignment 
 An ontology for the healthcare domain eases harmonising Medical, Life 
Sciences, and Pharma domains 
 Prominent vocabularies are already available as ontologies (SNOMED, OBI, EFO, 
RXNORM, Disease Ontology, Cell Type Ontology, etc.) 
 An ontology has limitations in representing 
 Contextual and modular information 
 Policy-based information 
424/24/451
Things cooking at the moment ! 
HL7 FHIR - OWL HL7 FHIR - RDF 
http://www.hl7.org/implement/standards/fhir/ 
43/44
Thank you 
Dr. Ratnesh Sahay 
Semantics in e-Health and Life Sciences (SeLS) 
Insight Centre for Data Analytics 
NUI Galway, The DERI building 
IDA Business Park, Lower Dangan 
Galway, IRELAND 
Tel: + 353 91 495253 
Fax: + 353 91 495541 
Web: http://www.ratneshsahay.org/ 
44/44

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Ontologising the Health Level Seven (HL7) Standard

  • 1. Ontologising the Health Level Seven (HL7) Standard Dr. Ratnesh Sahay Semantics in eHealth & Life Sciences (SeLS) Insight Centre for Data Analytics NUI Galway, Ireland Semantic Web Application and Tools 4 Life Science (SWAT4LS) Freie Universitaet Berlin Germany 09th December 2014
  • 2. HL7 Ontologies • Plug & Play Electronic Patient Records (PPEPR) – Funding: Enterprise Ireland – 2006-2009 – 2014: PPEPR-2 – http://www.ppepr.org/ – Lead by me • HL7 OWL – Supported by HL7 – 2013 - ongoing – http://gforge.hl7.org/gf/project/hl7owl/ – Lead by Lloyd McKenzie 2/44
  • 3. Tutorial Overview  Background  Ontology  Healthcare Interoperability  Health Level Seven (HL7) Messaging Environment  Plug and Play Electronic Patients Records (PPEPR)  Aligning HL7 Ontologies  Context & Modularity for HL7 ontologies 3/44
  • 4. Ontology ?  Humans like to classify things !  Galaxies, Molecules, Genomics, Education  The Latin term ontologia was first invented in 1613 by two German philosophers  Rudolf Gockel  Jacob Lorhard  In context of knowledge base systems – Tom Gruber (Siri inventor !)  Toward Principles for the Design of Ontologies Used for Knowledge Sharing (1993)  A Translation Approach to Portable Ontology Specifications (1995)  Ontologies are  „Explicit Specification of a conceptualisation.“ Tom Gruber, 1993  Agreed between groups with explicit semantics. OWL Semantics, W3C, 2004  Monotonic and make Open World Assumption (OWA). OWL Semantics, W3C, 2004  Good at Description of Reality and their mappings. 4/44
  • 5. Healthcare Interoperability: Background  1986: IEEE P1157 Medical Data Interchange (MEDIX) committee introduced the concept of a common healthcare data model  1987: HL7 Version 2  1995-2005: HL7 Version 3  MEDIX work is the core of current healthcare standards (Health Level Seven (HL7), openEHR, CEN 13606)  Health Level Seven (HL7) is the most widely deployed healthcare standard !  2000 onwards: HL7 Integration platforms  End-to-End bidirectional interface development (Mirth, iWay, iNTERFACEWARE)  Very few exit for Version 3 applications  None provided interoperability between Version 2 and Version 3 applications  2004 onwards: Semantic Interoperability (Ontologies) for Healthcare  Projects: Artemis, RIDE, SemanticHEALTH, SAPHIRE, ACGT, W3C HCLS, etc.  Plug and Play Electronic Patient Record (PPEPR) started end of 2006  Healthcare Vision: an Unified Electronic Healthcare Records (EHRs) 5/44
  • 6. Healthcare Interoperability: Current Situation Emergency Oncology Radiology Laboratory N*(N-1) Interfaces/Alignments 6/44
  • 7. Ontological Approaches EHR1 EHR2 EHR4 EHR3 (1) current situation (2) local alignment = (n× (n-1)) EHR1 EHR2 EHR4 EHR3 (1) ideal situation (2) global alignment EHR1 EHR2 EHR4 EHR3 (1) Hybrid approach (2) global and local alignments 7/44
  • 8. Example Scenario 4 Hospital A (Drug Policy) Messages EHR (Hospital B) 1 1 2 2 3 3 V2.6 EHR (Hospital A) 1 Observation Order Fulfilment Request 2 Observation Order Fulfilment Request Acknowledgement 3 Observation Promise Confirmation 4 5 5 4 5 4 Observation Order Complete (Test Results) EHR (General Practitioner) 5 Observation Order Complete Acknowledgement Sean Murphy Sean Murphy Diabetic patients are treated with either Insulin or Avandia, but not both. Sean Murphy 8/44
  • 9. Health Level Seven Standard (HL7)
  • 10. HL7 Messaging Environment - 1: Semantics to Implementation Semantics type PostalAddress alias AD specializes ANY, LIST<ADXP> { …… ……}; UML (Information Model ) XMLS (Implementation Technology) <xs:complexType name="AD" mixed="true"> <xs:complexContent> <xs:extension base="ANY"> <xs:sequence> <xs:element name="country" type="adxp.country"/> …… </xs:complexType> Top Middle Bottom HL7 Version 2 HL7 Version 3 AD ADXP ST ED ANY LIST<ADXP> 10/44
  • 11. Health Level Seven (HL7) Messaging Environment : - 2 Schema, Alignment, and Local Policies HL7 V3 Horizontal Alignments Hospital Hospital Vertical Alignments Vertical Alignments HL7 V2 < 90 complexTypes 50 elements/ attributes /> XSD (V2) Trial Policy Drug Policy Access Policy < 90 complexTypes 50 elements/ attributes /> XSD (V2) < 90 complexTypes 50 elements/ attributes /> XSD (V3) < 90 complexTypes 50 elements/ attributes /> XSD (V3) Medium size hospital with 300 – 380 beds 40,000 – 45,000 inpatients per year 65,000 – 70,000 outpatient per year 1000 – 1300 HL7 XSDs Drug Policy Bed Policy Access Policy 11/44
  • 12. HL7 Messaging Environment – 3: Contextual/Modular Information Structure Hospital B Drug Policy (2) Nursing domain (5) HL7 RIM (4) (Internal Objects) Code set (2) ID Schemes (1) Patient (345678IE) (1) (2) (3) Nursing domain (5) ID Schemes (1) Patient ID (1) (1) (2) (3)  Each entity is identified by an unique Object Identifiers (OIDs)  Health records are arranged in separate modules  Constraints or Policies are identifiable local modules Patient ID (2) HL7 Internal Objects with Unique OIDs Hospital A Drug Policy (2) Code set (1) Patient (678970W) HL7 RIM (3) (Internal Objects) HL7 Internal Objects with Unique OIDs 12/44
  • 13. HL7 Messaging Environment – 4: Example <affectedPerson codeSystem="2.5.1.76.1.1"> <name use="L"> <first>Sean</first> <last>Murphy</last> </name> </ affectedPerson> <identifiedPerson codeSystem=" 2.5.1.44.2.1 "> <name use="L"> <given>Sean</given> <family>Murphy</family> </name> </identifiedPerson> HL7 v3 UML XSD XML <PID.5> <XPN.3>Sean Murphy</XPN.3> <XPN.7>L</XPN.7> </PID.5> <PID.5> <XPN use=“S”> <XPN.1> Sean </XPN.1> <XPN.2> Murphy </XPN.2> </XPN> </PID.5> HL7 v2 XSD XML Context Hospital A: Patient.hasMedication (Insulin->intersection(Avandia))=isEmpty() Drug Policy 131/34/451
  • 14. Ontologising Health Level Seven Standard (HL7)
  • 15. Ontology Building Methodologies  Features Indentified  Reusability of non-ontological structured resources  Layering of ontologies  Local adaptation of ontologies Enterprise Ontology METHONTOLOGY On-To -Knowledge DILIGENT Reusability +/- +/- +/- +/- Layering - - - +/- Local Adaptation - - - + 151/54/451
  • 16. PPEPR Methodology Methodological DILIGENT PPEPR Methodology METHONTOLOGY Enterprise Ontology On-To-Knowledge Empirical Domain Experiences Road Maps 161/64/451
  • 17. PPEPR Methodology 9. Testing 3. Language Selection 4. Development Tools 5. Lift HL7 Resources 7. Local Adaptation Modelling Technology Support 6. Layering 1. Indentify Purpose 2. Indentify HL7 Resources Scoping 8. Alignment 171/74/451
  • 18. Modelling: Lifting HL7 Resources Language Transformation: A Hard problem XML Schema Ontology Data type (1) Supports large number of data types (1) RDFS/OWL 1 has limited support, thanks to OWL 2 for extended data types support Structure (1) Nested data structure (2) Tree structure ( top element is root) (3) Sequence to describe element order (1) Concept composition is through properties (2) Graph based (Any concept could be root) (3) No ordering of concepts Relation (1) Inheritance through Type and Extension (2) No Support (1) Multiple Inheritance (2) Inheritance on properties and logical implications (symmetric, Transitive, etc.) 181/84/451
  • 19. Transformation Rules  MIF2OWL  XSD2OWL element|attribute attribute element@substitutionGroup element@type type complexType|group|attributeGroup class | containedClass maximumMultiplicity| minimumMultiplicity @maxOccurs @minOccurs childClass extension@base|restriction@base union@memberTypes attribute@classCode type=Class HL7 MIF StaticModel.association| StaticModel.attribute Annotation@appinfo hl7:LongName|hl7:Type otherAnnotation | appInfo OWL ObjectProperty|DataProperty SubPropertyOf Range Class SubClassOf max|min Annotations@label|comment 191/94/451
  • 20. Example <xs:simpleType name="ActClassObservation"> <xs:annotation> <xs:documentation>specDomain: S11529 (C-0-T11527-S13856-S11529-cpt)</xs:documentation> </xs:annotation> <xs:union memberTypes="ActCondition ActClinicalTrial ActSpecimenObservation ActGenomicObservation "> </xs:union> </xs:simpleType> <xsl:for-each select="xsd:union[@memberTypes and parent::xsd:simpleType] | xsd:simpleContent/xsd:union[@memberTypes and parent::xsd:simpleContent“ ] <xsl:if test="@memberTypes"> <xsl:for-each select="tokenize(@memberTypes, 's')"> Class: <xsl:value-of select="." /> SubClassOf: <xsl:value-of select="$currentClass"/> </xsl:for-each> Class: ActCondition SubClassOf: ActObservation Class: ActClinicalTrial SubClassOf: ActObservation Class: ActSpecimenObservation SubClassOf: ActObservation Class: ActGenomicObservation SubClassOf: ActObservation 202/04/451
  • 21. Example <xs:complexType name="Patient"> <xs:sequence> <xs:element maxOccurs="unbounded" minOccurs="1" name="id" type="II"/> <xs:element maxOccurs="1" minOccurs="1" name="name" type="EN"/> <xs:element maxOccurs="1" minOccurs="1" name="administrativeGenderCode" type="CE"/> <xs:element maxOccurs="1" minOccurs="1" name="birthTime" type="TS"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="addr" type="AD"/> ..... </xs:sequence> <xs:attribute fixed="PSN" name="classCode" type="EntityPerson" use="optional"/> </xs:complexType> Class: <xsl:value-of select="$currentClass"/> <xsl:for-each select="xsd:attribute[@name="classCode"] <xsl:if test="@name='classCode'"> SubClassOf: <xsl:value-of select="@type"/> </xsl:for-each> Class: Patient SubClassOf: EntityPerson ObjectProperty: id Domain: Person Range: II ObjectProperty: name Domain: Person Range: EN ObjectProperty: administrativeGenderCode Domain: Person Range: CE ObjectProperty: birthTime Domain: Person Range: TS ObjectProperty: addr Domain: Person Range: AD 212/14/451
  • 22. Layering of Ontologies Top-down Bottom-up × Local Ontology Local Ontology Global Ontology (HL7 V2) Global Ontology (HL7 V3) × HL7 V2 (coreSchemas) HL7 V3 (coreSchemas) (1) Datatype (2) Vocabulary (common for all hospitals) Message Ontology + + Message Ontology Message Ontology Message Ontology HL7 V2 XSD(1) HL7 V2 XSD(2) HL7 V3 XSD(1) HL7 V3 XSD(2) Local Alignment Merging Message Schema (hospital-specific) Lifting Global Alignment Lifting 22/44
  • 23. Local Ontology: Merging Local Ontologies Class: ObservationRequest SubClassOf: ActObservation Class: SpecimenObservation SubClassOf: ActObservation Class: Observer SubClassOf: RoleClass Class: DiabeticType2Observation SubClassOf: SpecimenObservation Class: ObservationOrder.POOB_MT210000UV SubClassOf: ActObservation Class: Observer.POOB_MT210000UV SubClassOf: RoleClass Class: HemoglobinObservation.POOB_MT210000UV SubClassOf: ActObservation = = ⊑ Class: ObservationRequest SubClassOf: ActObservation + Class: SpecimenObservation SubClassOf: ActObservation Class: Observer SubClassOf: RoleClass Class: HemoglobinObservation.POOB_MT210000UV SubClassOf: ActObservation Class: DiabeticType2Observation SubClassOf: SpecimenObservation HemoglobinObservation.POOB_MT210000UV 232/34/451
  • 25. Alignment: HL7 Global and Local Ontologies HL7 v3 HL7 v2 GLOBAL LOCAL PID PDI XAD XON PID.5 XPN.1 XPN.2 Person Role Ad Organisation FirstName classCode Uni. Hospital Name LabTestOrder Id Pub. Hospital Name OBX1.2 identification GLOBAL LOCAL First Name LabTestOrder 25/44
  • 26. Alignment: Example Version 3 Version 3 Class: ObservationRequest SubClassOf: ActObservation Class: SpecimenObservation SubClassOf: ActObservation Class: Observer SubClassOf: RoleClass Class: DiabeticType2Observation SubClassOf: SpecimenObservation Class: ObservationOrder.POOB_MT210000UV SubClassOf: ActObservation Class: Observer.POOB_MT210000UV SubClassOf: RoleClass Class: HemoglobinObservation.POOB_MT210000UV SubClassOf: ActObservation Version 3 Version 2 Class: AD ObjectProperty: AD.1 Domain: AD Range: AD.1.CONTENT ObjectProperty: AD.2 Domain: AD Range: AD.2.CONTENT ObjectProperty: AD.3 Domain: AD Range: AD.3.CONTENT Class: AD SubClassOf: ANY ObjectProperty: streetAddressLine Domain: AD Range: Adxp.country ObjectProperty: state Domain: AD Range: Adxp.state ObjectProperty: city Domain: AD Range: Adxp.city <xsd:complexType name="AD.3.CONTENT"> <xsd:annotation> <xsd:appinfo> <hl7:Type>ST</hl7:Type> <hl7:LongName>City</hl7:LongName> </xsd:appinfo> </xsd:annotation> HL7 Annotation 262/64/451
  • 27. Ontology Alignment Tools Method/Tool HL7 (V3 –V3) precision-recall (Local Ontologies) HL7 (V2-V3) precision-recall (Global/Local Ontologies) Threshold Value Falcon-AO 70%(p)-60%(r) 70%(p)-50%(r) 70%(p)-50%(r) 30%(p)-30%(r) 30%(p)-20%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 H-Match 80%(p)-100%(r) 80%(p)-90%(r) 80%(p)-90%(r) 40%(p)-30%(r) 40%(p)-20%(r) 40%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 BLOOMS 90%(p)-40%(r) 90%(p)-30%(r) 90%(p)-30%(r) 90%(p)-20%(r) 90%(p)-10%(r) 90%(p)-10%(r) 0.1-0.4 0.4-0.7 0.7-1 RiMOM 60%(p)-100%(r) 70%(p)-90%(r) 70%(p)-90%(r) 40%(p)-40%(r) 40%(p)-40%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 AgreementMaker 70%(p)-100%(r) 70%(p)-90%(r) 70%(p)-90%(r) 40%(p)-50%(r) 40%(p)-50%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 27/44
  • 28. Alignment: SPARQL Recipes Class Matching CONSTRUCT { ?v3 owl:equivalentClass ?v2 } WHERE { ?v3 rdf:type owl:Class . ?v2 rdf:type owl:Class . ?v2 rdfs:label ?LongName . {FILTER regex(str(?v3), str(?LongName), ``i'')}} Property Matching CONSTRUCT { ?v3 owl:equivalentProperty ?v2 } WHERE { ?v3 rdf:type owl:ObjectProperty . ?v2 rdf:type owl:ObjectProperty . ?v2 rdfs:range ?v2range . ?v3 rdfs:range ?v3range . ?v2 rdfs:domain ?v2domain . ?v3 rdfs:domain ?v3domain . ?v2range owl:equivalentClass ?v3range . ?v2domain owl:equivalentClass ?v3domain }; 28/44
  • 29. Alignment: SPARQL Recipes Method/Tool HL7 (V3 –V3) precision–recall (Local Ontologies) HL7 (V2-V3) precision-recall (Global/Local Ontologies) Threshold Value Falcon-AO 70%(p)-60%(r) 70%(p)-50%(r) 70%(p)-50%(r) 30%(p)-30%(r) 30%(p)-20%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 H-Match 80%(p)-100%(r) 80%(p)-90%(r) 80%(p)-90%(r) 40%(p)-30%(r) 40%(p)-20%(r) 40%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 BLOOMS 90%(p)-40%(r) 90%(p)-30%(r) 90%(p)-30%(r) 90%(p)-20%(r) 90%(p)-10%(r) 90%(p)-10%(r) 0.1-0.4 0.4-0.7 0.7-1 RiMOM 60%(p)-100%(r) 70%(p)-90%(r) 70%(p)-90%(r) 40%(p)-40%(r) 40%(p)-40%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 AgreementMaker 70%(p)-100%(r) 70%(p)-90%(r) 70%(p)-90%(r) 40%(p)-50%(r) 40%(p)-50%(r) 30%(p)-20%(r) 0.1-0.4 0.4-0.7 0.7-1 SPARQL Recipes 80%(p)-90%(r) 50%(p)-60%(r) NA Extend alignment tools (AgreementMaker, RiMOM) by including domain-specific thematic structures instead of general information structures like WordNet, Wikipedia, DBpedia 29/44
  • 30. Context, Modularity and Local Policies
  • 31. Example Scenario PPEPR Hospital Drug Policy Messages Inconsistency Observation Order Fulfilment Request Observation Order Fulfilment Request Acknowledgement Observation Promise Confirmation Observation Order Complete (Test Results) Class: rxnorm:Avandia SubClassOf: galen:Drug Class: rxnorm:Insulin SubClassOf: galen:Drug EquivalentProperties: HospitalA:hasMedication HospitalB:EHR (Hospital hasTreatment B) 1 1 2 2 3 3 1 2 3 4 4 5 5 4 5 4 5 EHR (Hospital A) EHR (General Practitioner) DisjointClasses: HospitalA:hasMedication some rxnorm:Avandia HospitalA:hasMedication some rxnorm:Insulin Sean HospitalA:hasMedication rxnorm:Insulin Sean HospitalB:hasTreatment rxnorm:Avandia Observation Order Complete Acknowledgement 31/44
  • 32. Where is the Fault ?  Ontologies are  „Specification of a conceptualization.“ Tom Gruber, 1993  Agreed between groups with explicit semantics. OWL Semantics, W3C, 2004  Monotonic and make Open World Assumption (OWA). OWL Semantics, W3C, 2004  Good at Description of Reality and their mappings.  Ontology are not  Model of local and context-specific information  Model of time-dependent information  Model of context-specific constraints (e.g., policy, preferences) and validation 32/44
  • 33. State-OF-The-Art -1 : Formal Approaches  We did investigation for support of five features  Context-awareness (CA)  Modularity (M)  Profile and policy management (P & PM)  Correspondence expressiveness (CE)  Robustness to heterogeneity (RH) Considered Approaches:  Standard DL: Web Ontology Language (OWL)  No localised or contextualised semantics  Reusability or knowledge integration is limited to owl:imports  Context-Extensions of DLs : Distributed Description Logic (DDL)  Packet Description Logic (PDL)  Integrated Distributed Description Logic (iDDL)  E-connection  DL+Constraints/Rules  DL+DL-Safe Rules  Database-Style Integrity Constraints (IC) within OWL (OWL/IC in Pellet)  Rule-based  Modular Web Rule Bases  Query-Based  Query-Translation NONE OF THEM ADDRESSES ALL FEATURES  Repairing and Reasoning with Inconsistencies (DeLP) 33/44
  • 34. State-of-the-Art-2 (RDF)  Resource Description Framework (RDF)  RDF is an assertional logic (antecedent or premises is always true), where each triple expresses a simple proposition. [W3C RDF Semantics document] – In result, triple (s p o) represent facts, notion of “universal truth”. – RDF triples are context-free  Reification  N statements about a statement  Good for making statements about provenance  NO coupling with the truth of the triple that has been reified  Cannot relate the truth of a triple in one context (graph) to another  Named Graphs  Assigned an ID (URI) to each graph  Good for making statements about provenance  Associate named graphs with triples – Triples become quadruples – Fourth element is the URI of the named graph (origin)  Similar to Reification for the “truth of a triple”  N3-Context  Similar to Reification as far as “truth of a triple” is concerned 34/44
  • 35. Standard Semantics : OWL O=〈T,A〉 {0= ontology, T=Tbox, A=Abox} Class: rim:RolePatient SubClassOf: rim:Role Class: HA:IrishPPSId THA THB SubClassOf: rim:EntityIdentification Class: HA:LabTestOrder SubClassOf: rim:Act Class: HA:HemoglobinTest SubClassOf: rim:Act Class: galen:Patient SubClassOf: galen:Human Class: HB:OrderLabObservation SubClassOf: galen:OrderAct ObjectProperty: HB:hasTreatment DisjointClasses: HA:hasMedication some rxnorm:Avandia HA:hasMedication some rxnorm:Insulin Class: rxnorm:Avandia SubClassOf: galen:Drug Class: rxnorm:Insulin SubClassOf: galen:Drug = = = 353/54/451
  • 36. Distributed Description Logic (DDL) Oi=〈Ti,Ai, rij〉 {0i= ontology, Ti=Tbox, Ai=Abox, rij = Bridge Rules} Class: rim:RolePatient SubClassOf: rim:Role Class: HA:IrishPPSId THA THB = SubClassOf: rim:EntityIdentification Class: HA:LabTestOrder SubClassOf: rim:Act Class: HA:HemoglobinTest SubClassOf: rim:Act Class: galen:Patient SubClassOf: galen:Human Class: HB:OrderLabObservation SubClassOf: galen:OrderAct ObjectProperty: HB:hasTreatment DisjointClasses: = HA:hasMedication some rxnorm:Avandia HA:hasMedication some rxnorm:Insulin Class: rxnorm:Avandia SubClassOf: galen:Drug Class: rxnorm:Insulin SubClassOf: galen:Drug = HA:( HA:hasMedication some rxnorm:Insulin ) ⊑ HB:( HB:hasTreatment some rxnorm:Insulin ) HA:( not HA:hasMedication some rxnorm:Avandia ) ⊑ HB:( not HB: hasTreatment some rxnorm:Avandia) 363/64/451
  • 37. Packet Description Logic (PDL) Oi=〈Ti,Ai〉 {0i= ontology, Ti=Tbox, Ai=Abox} Class: rim:RolePatient SubClassOf: rim:Role Class: HA:IrishPPSId THA THB = SubClassOf: rim:EntityIdentification Class: HA:LabTestOrder SubClassOf: rim:Act Class: HA:HemoglobinTest SubClassOf: rim:Act Class: galen:Patient SubClassOf: galen:Human Class: HB:OrderLabObservation SubClassOf: galen:OrderAct ObjectProperty: HB:hasTreatment DisjointClasses: = HA:hasMedication some rxnorm:Avandia HA:hasMedication some rxnorm:Insulin Class: rxnorm:Avandia SubClassOf: galen:Drug Class: rxnorm:Insulin SubClassOf: galen:Drug = Class: ( HA:HemoglobinTest and (rim:measures some loinc: 4545-4) ) EquivalentTo: ( galen:BloodSugarTest and (HB:hasCode some snomed: 43396009) ) 373/74/451
  • 38. Database Style-IC O=〈Tn, TC, A〉 {0= ontology, Tn =Normal Tbox,TC = Constraint Tbox, A=Abox} Class: rim:RolePatient SubClassOf: rim:Role Class: HA:IrishPPSId SubClassOf: rim:EntityIdentification Class: HA:LabTestOrder SubClassOf: rim:Act Class: HB:HemoglobinTest SubClassOf: rim:Act Class: galen:Patient SubClassOf: galen:Human Class: HB:OrderLabObservation SubClassOf: galen:OrderAct ObjectProperty: HB:hasTreatment DisjointClasses: HA:hasMedication some rxnorm:Avandia HA:hasMedication some rxnorm:Insulin Class: rxnorm:Avandia SubClassOf: galen:Drug Class: rxnorm:Insulin SubClassOf: galen:Drug Tn(HA) = = = Tn(HB) TC(HA) 383/84/451
  • 39. Feature Comparisons Context-awareness Modularity Profile & Policy Management DL/OWL - -/+ - DDL/C-OWL + + - P-DL + + - DDL Revisited + + - IDDL + + - E-connection + + - RDFS-C (Guha’s) + -/+ - Query-based -/+ - - Modular Rule bases + + -/+ OWL/IC - -/+ -/+ DeLP/Paraconsistent - - -/+ 39/44
  • 40. Envisioned Situation - Context & Policy aware ontological model and reasoning GALEN SNOMED RIM Global (D) Policy1 Policy2 Policy3 Policyn Local (P) GALEN SNOMED RIM Local (P) Global (D) Hospital A Hospital B Policy1 Policy2 Policy3 Policyn 414/14/451
  • 41. Summary  An ontology is good at the top-down modeling of a domain  reduces the bilateral correspondences between healthcare applications  delegates the majority of mediation to the central integration location  An ontology provides an executable (comparing to HL7 UML model) semantics and consistent model  The Semantic Web layer cake allows to engage information model, schema, and instances under a single framework. In HL7 they are represented in three isolated layers.  An automated ontology alignment is a great support for the domain experts comparing manual syntactic alignment  An ontology for the healthcare domain eases harmonising Medical, Life Sciences, and Pharma domains  Prominent vocabularies are already available as ontologies (SNOMED, OBI, EFO, RXNORM, Disease Ontology, Cell Type Ontology, etc.)  An ontology has limitations in representing  Contextual and modular information  Policy-based information 424/24/451
  • 42. Things cooking at the moment ! HL7 FHIR - OWL HL7 FHIR - RDF http://www.hl7.org/implement/standards/fhir/ 43/44
  • 43. Thank you Dr. Ratnesh Sahay Semantics in e-Health and Life Sciences (SeLS) Insight Centre for Data Analytics NUI Galway, The DERI building IDA Business Park, Lower Dangan Galway, IRELAND Tel: + 353 91 495253 Fax: + 353 91 495541 Web: http://www.ratneshsahay.org/ 44/44