Ontologising the Health Level Seven (HL7) Standard
This relates to my PhD work [1] but now gaining momentum….good to see that.
[1]http://aran.library.nuigalway.ie/xmlui/bitstream/handle/10379/3034/ratnesh.sahay_PhDThesis.pdf?sequence=1
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(Note: This is a very dated version of this popular deck, as SlideShare does not provide authors with a mechanism to update their documents. If interested in the latest version, feel free to message me on LinkedIn or at wweinmeyer@gmail.com. Also, feel free to ask SlideShare to bring back the ability to update posted documents.)
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Splunking HL7 Healthcare Data for Business ValueSplunk
Healthcare data is time-oriented and diverse. HL7 (Health Level Seven International) is a set of interoperability standards, formats and definitions for exchanging data between software applications used by healthcare providers. In this session, learn how to leverage HL7 data for business value. Through a presentation and demo’s, we will discuss a variety of HL7 use cases from exploring HL7 data within Splunk, addressing missing orders investigations, queuing up integrations, and others. Also, you can learn about the health of the system that is providing these services by using Splunk ITSI.
How do you protect the data in big data analytics projects?
As big data initiatives focus on volume, velocity or variety of data, often overlooked in the big data project is the security of the data. This is especially important for financial services, healthcare and government or anytime sensitive data is analyzed.
This webinar highlights:
*Hadoop security landscape
*Hadoop encryption, masking, and access control
*Customer examples of securing hadoop environments
This slide deck is about automated testing of BizTalk HL7 solutions and showing how you can use behaviour driven acceptance tests to automate your testing
This tutorial provides an introduction to the major HL7 RIM derived and RIM influenced standards. The student will also learn key aspects of the HL7 V3 Development Framework (HDF).
Topics Covered:
1. HL7 Development Framework
2. HDF Methodology
3. HL7 V3 Development Artifacts
4. Sample V3 Clients and Projects
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What if…
…your data stores were limitless and accessible?
…data discovery was fast… really fast?
…connectivity was so seamless you could almost take it for granted?
And what if you could do all this with your preferred BI tool?
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Securing Hadoop's REST APIs with Apache Knox Gateway Hadoop Summit June 6th, ...Kevin Minder
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Basic web service terminology: HTTP, SOAP, WSDL, RPC vs Document styles
Consuming web services from the Oracle Database options
Investigation of utl_http and utl_dbws
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An introduction to fundamental architecture conceptswweinmeyer79
(Note: This is a very dated version of this popular deck, as SlideShare does not provide authors with a mechanism to update their documents. If interested in the latest version, feel free to message me on LinkedIn or at wweinmeyer@gmail.com. Also, feel free to ask SlideShare to bring back the ability to update posted documents.)
A discussion of the fundamentals you need to nail in your architecture practice:
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You are free to use/copy this information but if you do so, please include an acknowledgement
Presented at the 8th Healthcare CIO Certificate Program, Hospital Administration School, Faculty of Medicine Ramathibodi Hospital, Mahidol University on March 21, 2018
Presented at the 7th Healthcare CIO Certificate Program, Hospital Administration School, Faculty of Medicine Ramathibodi Hospital, Mahidol University on September 15, 2016
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Andy leads the HAVAS HEALTH SOFTWARE team of software engineers to develop solutions that focus on the best possible outcome for the end user that ensure the business needs are met.
@andystopford
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Similar to Ontologising the Health Level Seven (HL7) Standard (20)
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https://pubrica.com/academy/case-study-or-series/how-many-patients-does-case-series-should-have-in-comparison-to-case-reports/
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Defecation
Normal defecation begins with movement in the left colon, moving stool toward the anus. When stool reaches the rectum, the distention causes relaxation of the internal sphincter and an awareness of the need to defecate. At the time of defecation, the external sphincter relaxes, and abdominal muscles contract, increasing intrarectal pressure and forcing the stool out
The Valsalva maneuver exerts pressure to expel faeces through a voluntary contraction of the abdominal muscles while maintaining forced expiration against a closed airway. Patients with cardiovascular disease, glaucoma, increased intracranial pressure, or a new surgical wound are at greater risk for cardiac dysrhythmias and elevated blood pressure with the Valsalva maneuver and need to avoid straining to pass the stool.
Normal defecation is painless, resulting in passage of soft, formed stool
CONSTIPATION
Constipation is a symptom, not a disease. Improper diet, reduced fluid intake, lack of exercise, and certain medications can cause constipation. For example, patients receiving opiates for pain after surgery often require a stool softener or laxative to prevent constipation. The signs of constipation include infrequent bowel movements (less than every 3 days), difficulty passing stools, excessive straining, inability to defecate at will, and hard feaces
IMPACTION
Fecal impaction results from unrelieved constipation. It is a collection of hardened feces wedged in the rectum that a person cannot expel. In cases of severe impaction the mass extends up into the sigmoid colon.
DIARRHEA
Diarrhea is an increase in the number of stools and the passage of liquid, unformed feces. It is associated with disorders affecting digestion, absorption, and secretion in the GI tract. Intestinal contents pass through the small and large intestine too quickly to allow for the usual absorption of fluid and nutrients. Irritation within the colon results in increased mucus secretion. As a result, feces become watery, and the patient is unable to control the urge to defecate. Normally an anal bag is safe and effective in long-term treatment of patients with fecal incontinence at home, in hospice, or in the hospital. Fecal incontinence is expensive and a potentially dangerous condition in terms of contamination and risk of skin ulceration
HEMORRHOIDS
Hemorrhoids are dilated, engorged veins in the lining of the rectum. They are either external or internal.
FLATULENCE
As gas accumulates in the lumen of the intestines, the bowel wall stretches and distends (flatulence). It is a common cause of abdominal fullness, pain, and cramping. Normally intestinal gas escapes through the mouth (belching) or the anus (passing of flatus)
FECAL INCONTINENCE
Fecal incontinence is the inability to control passage of feces and gas from the anus. Incontinence harms a patient’s body image
PREPARATION AND GIVING OF LAXATIVESACCORDING TO POTTER AND PERRY,
An enema is the instillation of a solution into the rectum and sig
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One of the most developed cities of India, the city of Chennai is the capital of Tamilnadu and many people from different parts of India come here to earn their bread and butter. Being a metropolitan, the city is filled with towering building and beaches but the sad part as with almost every Indian city
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VERIFICATION AND VALIDATION TOOLKIT Determining Performance Characteristics o...
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
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
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
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
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
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
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
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42. Things cooking at the moment !
HL7 FHIR - OWL HL7 FHIR - RDF
http://www.hl7.org/implement/standards/fhir/
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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/
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