data warehousing with semantic...
TRANSCRIPT
![Page 1: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/1.jpg)
Data Warehousing with Semantic Ontologies
April 13, 2015, Session: 54 Richard E. Biehl, Ph.D. CSQE, CSSBB
Data-Oriented Quality Solutions DISCLAIMER: The views and opinions expressed in this presentation are those of the author and do not necessarily represent official policy or position of HIMSS.
![Page 2: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/2.jpg)
Conflict of Interest Richard E. Biehl, Ph.D. Ownership Interest: Richard is the sole proprietor of Data-Oriented Quality Solutions (DOQS), an IT/Quality consulting practice founded in 1988 and operating out of Orlando, Florida, USA. Consulting Fees: Richard earns approximately 15% of his income from consulting engagements that involve the heuristics included in this presentation. Other: The heuristics in this presentation can be immediately and directly implemented by attendees. Nothing has been held back that would necessitate engaging DOQS for implementation.
© HIMSS 2015 2
![Page 3: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/3.jpg)
Learning Objectives 1. Demonstrate how the HIT human-machine interface relies on the semantic
abilities of human participants
2. Categorize the three semantic layers relevant to clinical data warehouse design
3. Employ an ontological framework for mapping and modeling system-practice-phenotype data
4. Illustrate how semantic ontologies can resolve common problems in warehousing, using the ICD-9 to ICD-10 conversion problem as an example
5. Propose a reasoning-based warehouse design that can learn on behalf of human participants who are increasingly overwhelmed by the flow of big data
3
![Page 4: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/4.jpg)
Mapping to STEPS™
http://www.himss.org/ValueSuite
We start here!
4
![Page 5: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/5.jpg)
Previous HIMSS Presentations Fundamentals of Data Warehousing in Healthcare 2013 HIMSS Annual Conference, New Orleans Implementing a Healthcare Data Warehouse in One year (Or Less) 2012 HIMSS Annual Conference, Las Vegas Standardizing Data Dimensions of Healthcare Data Warehouses 2010 HIMSS Annual Conference, Atlanta Success by Design: Effective Data Quality Measurements in a Hospital Data Warehouse 2008 HIMSS Annual Conference, Orlando
Data Quality
Data Dimensions
Project Management
Warehouse Design
5
![Page 6: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/6.jpg)
“Big Data” is about… • New data base architectures and performance challenges, • New analytical paradigms and ways of seeing the world through
data, • New design patterns for bringing together and using vast amounts of
data, • New social and ethical challenges that need to be addressed within
all of these new opportunities, • And all of the everyday mundane issues of systems and software
engineering that we’ve always been challenged to address, writ large.
6
![Page 7: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/7.jpg)
The Central Challenge • “Big Data” increases the urgency of having strong control over our
information. • The human-machine interface relies on the semantic abilities of the
human participant. • We need to engineer controlled semantics into our systems… • We want systems that can reason and learn on behalf of the human
participant that is increasingly overwhelmed by the volume and flow of big data.
X
7
![Page 8: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/8.jpg)
Semantic Layers in a Biomedical Data Warehouse
• System – What is in the dataset or message?
• Practice – What is the provider doing or thinking?
• Phenotype – What’s right or wrong with the patient?
8
![Page 9: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/9.jpg)
An Ontological Framework
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology of General Medical Science (OGMS)
Ontology for Biomedical
Investigation (OBI)
Hypotheses & Conclusions Observations
Biomedical Semantics Biomedical Syntax
Biomedical Epistemology
9
![Page 10: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/10.jpg)
Continuant Occurrent
Entity
Basic Formal Ontology
10
![Page 11: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/11.jpg)
Independent Continuant
Continuant
Spatial Region
Dependent Continuant
Specifically Dependent Continuant
Generically Dependent Continuant
Quality Realizable Entity
Disposition Function Role
Material Entity
Object Boundary Site
Object Aggregate Object Fiat
Object Part
Basic Formal Ontology
11
![Page 12: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/12.jpg)
Basic Formal Ontology
Occurrent
Processual Entity
Spatiotemporal Region
Temporal Region
Process Aggregate Process Fiat
Process Part Processual
Context Processual Boundary
12
![Page 13: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/13.jpg)
Basic Formal Ontology
13
HIMSS10
HIMSS13
![Page 14: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/14.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
What is in the dataset or message?
14
![Page 15: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/15.jpg)
Independent Continuant
Specifically Dependent Continuant
Generically Dependent Continuant
Material Information
Bearer
Information Content Entity
Information Carrier
Dependent Continuant
Continuant
Basic Formal Ontology (BFO)
Information Artifact Ontology (IAO)
15
![Page 16: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/16.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology for Biomedical
Investigation (OBI)
What is in the dataset or message?
What is the provider doing or thinking?
16
![Page 17: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/17.jpg)
Independent Continuant
Specifically Dependent Continuant
Age
Basic Formal Ontology (BFO)
Ontology for Biomedical
Investigations (OBI)
Dependent Continuant
Continuant
Organism
Diagnosis Generically Dependent Continuant
Patient Role
Biological Sex
Role
Quality
Alive
17
![Page 18: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/18.jpg)
Process
Performing a diagnosis
Performing an assessment
Collection of specimen
Administration of material
Processual Context
Hospital Encounter
Office Visit Occurrent
Basic Formal Ontology (BFO)
Ontology for Biomedical Investigations (OBI)
Process Aggregate Laboratory
Test
Medication Course
Transplant Surgery
18
![Page 19: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/19.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology of General Medical Science (OGMS)
Ontology for Biomedical
Investigation (OBI)
What is in the dataset or message?
What is the provider doing or thinking?
What’s right or wrong with the patient?
19
![Page 20: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/20.jpg)
Object Aggregate
Organism Population
Continuant Extended Organism
Object Organism
Basic Formal Ontology (BFO)
Ontology for General Medical Science
(OGMS)
Occurrent
Process
Disease Course
Pathological Bodily
Process
Processual Context Lifespan
Process Aggregate
20
![Page 21: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/21.jpg)
Independent Continuant
Extended Organism
Specifically Dependent Continuant
Disease
Occurrent
Processual Entity
Disease Course
Pathological Bodily Process
Sign or Symptom
Continuant
Extended Organism experiences Disease Course instance of a Disease resulting from a Disorder with disposition toward Pathological Bodily Process which produces Pathological Anatomical Structure recognized as Sign or Symptom
Disorder
Pathological Anatomical Structure
Process Aggregate
Basic Formal Ontology (BFO)
Ontology for General Medical Science
(OGMS)
21
![Page 22: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/22.jpg)
Independent Continuant
Specifically Dependent Continuant
Disorder
Disease
Basic Formal Ontology (BFO)
Ontology for General Medical Science
(OGMS)
Dependent Continuant
Continuant Extended Organism
Occurrent Processual Entity
Disease Course
Diagnostic Process
Pathological Bodily
Process
Diagnosis Generically Dependent Continuant
Information Content Entity
Pathological Anatomical Structure
Sign or Symptom
expe
rienc
es
Age
Ontology for Biomedical
Investigations (OBI)
Organism
Performing a diagnosis
Diagnosis
Patient Role
Biological Sex
Alive
Role
Quality
Material Information
Bearer
Information Carrier
Information Artifact Ontology (IAO)
22
![Page 23: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/23.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology of General Medical Science (OGMS)
Ontology for Biomedical
Investigation (OBI)
Hypotheses &
Conclusions Observations
Biomedical Epistemology
Biomedical Semantics Biomedical
Syntax
23
![Page 24: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/24.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology of General Medical Science (OGMS)
Ontology for Biomedical
Investigation (OBI)
Biomedical Semantics Biomedical
Syntax Raw message
Data from a clinical process about a patient
A clinical view of the patient
Inbound messages (e.g., CCD) are mapped as field-level information artifacts back to the clinical processes that evaluated the patient.
The contents of those messages – the values of those information artifacts – are then mapped into a clinical picture of the patient.
The three mid-level ontologies are mapped to each other through the common BFO framework. The values in the messages end up being at a different ontological level than the semantic meaning of those values, allowing for translation, harmonization, and quality control to intervene as systems data in messages is translated into clinical data in systems.
top level
mid-level
24
![Page 25: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/25.jpg)
Information Artifact Ontology
(IAO)
Basic Formal Ontology (BFO)
Ontology of General Medical Science (OGMS)
Ontology for Biomedical
Investigation (OBI)
Biomedical Semantics Biomedical
Syntax
top level
mid-level
domain -level
SNOMED, ICD, CPT, RxNORM, LOINC, MeSH, etc.
25
![Page 26: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/26.jpg)
Ontology-Based Design
•Source ETL analysis & mapping •Warehouse logical database design •Post-load spider processing •Conducting queries & analysis
26
![Page 27: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/27.jpg)
<ClinicalDocument xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="urn:hl7-org:v3“xmlns:cda="urn:hl7-org:v3" xmlns:sdtc="urn:hl7-org:sdtc“><realmCode code="US"/><typeId root="2.16.840.1.113883.1.3" extension="POCD_HD000040"/><!-- US General Header Template --><templateId root="2.16.840.1.113883.10.20.22.1.1“ /><templateId root="2.16.840.1.113883.10.20.22.1.2"/><id extension="TT988" root="2.16.840.1.113883.19.5.99999.1"/><code codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" code="34133-9“ displayName="Summarization of Episode Note"/><title>Community Health and Hospitals: Health Summary</title><effectiveTime value="201209150000-0400"/><confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25"/><languageCode code="en-US"/><setId extension="sTT988“ root="2.16.840.1.113883.19.5.99999.19"/><versionNumber value="1"/> <component><structuredBody><component><section><templateId root="2.16.840.1.113883.10.20.22.2.5"/><templateId root="2.16.840.1.113883.10.20.22.2.5.1"/><code code="11450-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC“ displayName="PROBLEM LIST"/><title>PROBLEMS</title><entryRelationship typeCode="SUBJ" inversionInd="true“><observation classCode="OBS" moodCode="EVN“><templateId root="2.16.840.1.113883.10.20.22.4.31"/><code code="445518008“ codeSystem="2.16.840.1.113883.6.96“ displayName="Age At Onset"/> <statusCode code="completed"/> <value xsi:type="PQ" value="57" unit="a"/> </observation></entryRelationship></entry></section></component><structuredBody></component></clinicalDocument>
Age at Onset 57 years
27
![Page 28: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/28.jpg)
section
<type> " CD" <codeSystem> “2.16.840.1.113883.6.96”
<displayName> “Pneumonia”
value
<code> " 233604007"
statusCode <code> “completed”
effectiveTime
Low <value> " 20080103" High <value> "20080103"
<code> "409586006"
<codeSystem> “2.16.840.1.113883.6.96”
<displayName> “Complaint”
code
id <root> "ab1791b0-5c71-11db-b0de-0800200c9a66"
templateId <root> "2.16.840.1.113883.10.20.22.4.4"
observation
<classCode> “OBS"
<moodCode> “EVN"
entryRelationship <typeCode> “SUBJ"
<title> “PROBLEMS"
<codeSystemName> " CD"
<codeSystem> “2.16.840.1.113883.6.1”
<displayName> “PROBLEM LIST”
code
<code> "11450-4"
templateId <root> "2.16.840.1.113883.10.20.22.2.5"
templateId <root> "2.16.840.1.113883.10.20.22.2.5.1“
entry <typeCode> “DRIV"
act
id <root> "ec8a6ff8-ed4b-4f7e-82c3-e98e58b45de7"
templateId <root> "2.16.840.1.113883.10.20.22.4.3” <classCode> “ACT"
<moodCode> “EVN"
<code> “CONC"
<codeSystem> “2.16.840.1.113883.5.6”
<displayName> “Concern”
code
statusCode <code> “completed”
effectiveTime
Low <value> " 20080103" High <value> "20080103"
![Page 29: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/29.jpg)
observation
<code> "33999-4"
<codeSystem> “2.16.840.1.113883.6.1”
<displayName> “Status”
code
<classCode> “OBS"
<moodCode> “EVN"
templateID <root> “2.16.840.1.113883.10.20.22.4.6”
statusCode <code> “completed”
entryRelationship <typeCode> “REFR"
id <root> “ab1791b0-5c71-11db-b0de-0800200c9a66”
effectiveTime
Low <value> "20080103" High <value> “20090227130000+0500"
<type> " CD" <codeSystem> “2.16.840.1.113883.6.96”
<displayName> “Resolved”
value
<code> " 413322009”
observation
<value> “57” <unit> “a” <type> “PQ” Value
<code> "445518008"
<codeSystem> “2.16.840.1.113883.6.96”
<displayName> “Age At Onset”
code
<classCode> “OBS"
<moodCode> “EVN" <root> “2.16.840.1.113883.10.20.22.4.31”
templateID
statusCode <code> “completed”
entryRelationship <typeCode> “SUBJ" <inversionInd> “true"
act
![Page 30: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/30.jpg)
observation
<code> “11323-3" <codeSystem> “2.16.840.1.113883.6.1”
<displayName> “Health Status”
code
<classCode> “OBS"
<moodCode> “EVN"
templateID <root> “2.16.840.1.113883.10.20.22.4.5”
statusCode <code> “completed”
entryRelationship <typeCode> “REFR"
id <root> “ab1791b0-5c71-11db-b0de-0800200c9a66”
effectiveTime
Low <value> " 20080103" High <value> " 20090227130000+0500"
<type> " CD" <codeSystem> “2.16.840.1.113883.6.96”
<displayName> “Alive and well”
value
<code> "81323004”
<codeSystemName> "LOINC"
<codeSystemName> “SNOMED CT"
30
![Page 31: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/31.jpg)
Material Information
Bearer CCD XML 31
![Page 32: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/32.jpg)
Information Content Entity
Problem Observation
<code>
Age Observation <value>
Problem Observation <start>
Problem Observation <stop>
Generically Dependent Continuant
Material Information
Bearer CCD XML 32
![Page 33: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/33.jpg)
Complaint (409586006)
Start Time (398201009)
Stop Time (397898000)
Information Content Entity
Problem Observation
<code>
Age Observation <value>
Problem Observation <start>
Problem Observation <stop>
is a
bout
is a
bout
is a
bout
Age At Onset (445518008)
is a
bout
Generically Dependent Continuant
Material Information
Bearer CCD XML
SNOMED (Functional
Classes)
33
![Page 34: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/34.jpg)
Complaint (409586006)
Start Time (398201009)
Stop Time (397898000)
Information Content Entity
Problem Observation
<code>
Age Observation <value>
Problem Observation <start>
Problem Observation <stop>
is a
bout
is a
bout
is a
bout
Information Carrier
“2006-03-22” “2006-04-22" "409586006“ “Complaint”
Age At Onset (445518008)
is a
bout
“29”
Specifically Dependent Continuant
Generically Dependent Continuant
Material Information
Bearer CCD XML
SNOMED (Functional
Classes)
34
![Page 35: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/35.jpg)
Complaint (409586006)
Start Time (398201009)
Stop Time (397898000)
age_at_onset
date_low
date_high
type
ProblemSchema:
coded diagnosis
Information Content Entity
Problem Observation
<code>
Age Observation <value>
Problem Observation <start>
Problem Observation <stop>
is a
bout
is a
bout
is a
bout
Information Carrier
“2006-03-22” “2006-04-22" "409586006“ “Complaint”
Age At Onset (445518008)
is a
bout
“29”
Specifically Dependent Continuant
Generically Dependent Continuant
Material Information
Bearer CCD XML
SNOMED (Functional
Classes)
35
![Page 36: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/36.jpg)
type Complaint
date_high 2006-04-22
date_low 2006-03-22
Problem: 480.0
Pneumonia due to adenovirus
Complaint (409586006)
Start Time (398201009)
Stop Time (397898000)
age_at_onset
date_low
date_high
type
ProblemSchema:
coded diagnosis
Information Content Entity
Problem Observation
<code>
Age Observation <value>
Problem Observation <start>
Problem Observation <stop>
is a
bout
is a
bout
is a
bout
Information Carrier
“2006-03-22” “2006-04-22" "409586006“ “Complaint”
Age At Onset (445518008)
is a
bout
“29”
Specifically Dependent Continuant
Generically Dependent Continuant
Material Information
Bearer CCD XML
age_at_onset 29
SNOMED (Functional
Classes)
36
![Page 37: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/37.jpg)
Information Artifact Ontology (IAO)
//section/templateId /@root="2.16.840.1.113883.10.20.22.2.5.1”
ClinicalDocument/templateId/@root="2.16.840.1.113883.10.20.22.1.2"
//entry/@typeCode="DRIV“ //act/@classCode="ACT“
//@moodCode="EVN“ //templateId/@root="2.16.840.1.113883.10.20.22.4.3
" //code //effectiveTime
//low //high
@code
@value //entryRelationship/@typeCode="SUBJ“ //observation/@classCode="OBS"
//@moodCode="EVN“ //templateId/@root="2.16.840.1.113883.10.20.22.4.4"
@value
@codeSystem
//code @code @codeSystem
//value @code @ codeSystem
@type
Information Content Entity Information
Carrier
"CONC"
"20070103" "20070103"
"2.16.840.1.113883.5.6
"409586006" "2.16.840.1.113883.6.96"
“233604007” " 2.16.840.1.113883.6.96
“CD”
Concern
Complaint
Problem List
Pneumonia
//entryRelationship/@typeCode=“SUBJ“ @inversionInd“true"
//observation/@classCode="OBS" //@moodCode="EVN“
//templateId/@root="2.16.840.1.113883.10.20.22.4.31" //code @code @codeSystem
"445518008 " "2.16.840.1.113883.6.96"
//value @unit @type
@value “a” “PQ
“57” Age at Onset 57 years
Summarization of Episode
Note
37
![Page 38: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/38.jpg)
Concern
Complaint
Resolved
Age at Onset 57 years
Active
Problem List
Asthma
Pneumonia
Status
Alive & Well
Health Status
38
![Page 39: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/39.jpg)
Concern
Status
Problem List
Resolved
Age at Onset 57 years
Summarization of Episode Note
Class with related value
Class with embedded attribute value
Classes can include classes below them in the ICE mappings Metadata Layer
Defines the meaning of the entryRelationship at the next highest layer
Contains entryRelationships with variable meaning
39
![Page 40: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/40.jpg)
Concern
Resolved
Active
Status
Concern
Resolved
Active
Status
Status
enRel
enRel
40
![Page 41: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/41.jpg)
Concern
Resolved
Age at Onset 57 years Active
Problem List
Asthma
Pneumonia Alive & Well
Status Complaint Age Health Status
Status Complaint Age Health Status
Under this scenario, there would no longer be classes or tables for the various LOINC codes that define the semantics of each <entryRelationship>. They instead become the schema definition for the <entry> In which they are found.
A schema entry is an IAO Information Carrier that has been mapped to a BFO Generically Dependent Continuant (GDC).
41
![Page 42: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/42.jpg)
Information Artifact Ontology (IAO)
ClinicalDocument/templateId/@root="2.16.840.1.113883.10.20.22.1.2"
Information Content Entity
Information Carrier
//recordTarget//patientRole
Summarization of Episode Note
@extension
@root
“MRN1234567”
"2.16.840.1.113883.19.5.2"
//Id
Medical Record Number (MRN)
(2.16.840.1.113883.19.5.2)
MRN (398225001)
Patient Role
Patient-related Identification code
(422549004)
//section/templateId /@root="2.16.840.1.113883.10.20.22.2.5.1”
Problem List
Individual organism identifier
MRN
CRID
42
Protected
![Page 43: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/43.jpg)
“Isabella Jones”
Patient Name (371484003)
Information Content Entity
Information Carrier
Specifically Dependent Continuant
Generically Dependent Continuant recordTarget
MRN <id extension>
MRN (398225001)
SSN <id extension>
"998991" "111-00-2330" is
abo
ut
is a
bout
Tax ID (12345654)
patientRole <name>
Organism
Patient Role
Continuant
Role
Independent Continuant
Taxpayer Role
inheres in
Protected
43
![Page 44: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/44.jpg)
“Isabella Jones”
Patient Name (371484003)
Information Content Entity
Information Carrier
Specifically Dependent Continuant
Generically Dependent Continuant recordTarget
MRN <id extension>
MRN (398225001)
SSN <id extension>
"998991" "111-00-2330" is
abo
ut
is a
bout
Tax ID (12345654)
patientRole <name>
Organism
Patient Role
Continuant
Role
Independent Continuant
Taxpayer Role
inheres in
PHI PHI PHI
Protected
44
![Page 45: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/45.jpg)
Organism
Patient Role
Continuant
Role
Independent Continuant
Biospecimen
derived from Object Aggregate
Object
Extended Organism
inheres in
includes
MRN (398225001)
Accession Number
identifies
identifies
extends
Occurrent
Assigning a centrally
registered Id
Organization
Specimen Role
inheres in
participates in
Individual organism identifier
Specimen identifier
Information Content Entity
Generically Dependent Continuant
MRN
is about
is about
CRID instantiates
PHI
PHI Protected
Secure any continuant that identifies something in which a protected role inheres, or anything extending or derived from such a continuant.
![Page 46: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/46.jpg)
mappingRelation
closeMatch
broadMatch narrowMatch
relatedMatch
exactMatch
inverseOf
symmetric symmetric
symmetric transitive
disjoint
Simple Knowledge Organization System (SKOS)
46
![Page 47: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/47.jpg)
LM
L
LMN
XY closeMatch
1
isA
isA
broadMatch
narrowMatch
Assertion: XY closeMatch1 LM Known: LM isA L LMN isA LM Implied: L narrowMatch XY LMN broadMatch XY By inverse rule: XY broadMatch L XY narrowMatch LMN
broadMatch
narrowMatch
1 Any ontology edge that has been curated to closeMatch would have the same
implications.
47
![Page 48: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/48.jpg)
LOINC 882-1 “ABO + Rh group, Blood”
CPT 86901 “Blood typing;
Rh (D)”
CPT 86900 “Blood typing; ABO”
LOINC 884-7 “ABO + Rh group, Blood Capillary”
LOINC 34474-7 “ABO + Rh group, Cord Blood”
CPT to LOINC
48
![Page 49: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/49.jpg)
84.71 ICD-9CM Application of external fixator device, monoplanar system
79.21 ICD-9CM Open reduction of fracture without internal fixation, humerus
78.12 ICD-9CM Application of
external fixator device,
humerus
0PSD0BZ ICD10PCS Reposition Left Humeral Head with Monoplanar
External Fixation Device, Open Approach
0PSC0BZ ICD10PCS Reposition Right Humeral
Head with Monoplanar External Fixation Device,
Open Approach
ICD-9 to ICD-10
49
![Page 50: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/50.jpg)
Rosuvastatin
Crestor
Crestor . tradenameOf . Rosuvastatin {broadMatch} Rosuvastatin . hasTradename . Crestor {narrowMatch}
RxNorm
50
![Page 51: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/51.jpg)
Crestor 320864
RxNORM
Crestor Pill 1173053
has_ingredient
Clinical D
rug Rosuvastatin
301542
Organic C
hemical
Pharm
acologic Substance
Biologically A
ctive Substance
Rosuvastatin calcium 323828
has_form
has_tradename
form_of
precise _ingredient_of
Rosuvastatin calcium 5 MG
859423
has_precise _ingredient
has_ingredient
Rosuvastatin calcium 5 MG Oral
Tablet 859424
consists_of consititutes
Rosuvastatin calcium 5 MG Oral
Tablet [Crestor] 859426
Rosuvastatin calcium 5 MG
[Crestor] 859423
consists_of
consists_of
has_ingredient
isA
Oral Tablet
has_does_form
has_tradename
has_precise _ingredient
isA
Crestor Oral Product
isA
rosuvastatin Oral Tablet [Crestor]
isA
The mess!
51
![Page 52: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/52.jpg)
Refractory Migraine
(423894005)
Lower Half Migraine
(26150009)
Migraine (37796009)
Vascular Headache
(128187005)
Headache Disorder
(340461009)
Headache (25064002)
has_definitional_manifestation
52
![Page 53: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/53.jpg)
Refractory Migraine
(423894005)
Lower Half Migraine
(26150009)
Migraine (37796009)
Vascular Headache
(128187005)
Headache Disorder
(340461009)
Headache (25064002)
has_definitional_manifestation
Headache (748.0)
Migraine (346)
Migraine, unspecified
(346.9)
53
![Page 54: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/54.jpg)
Refractory Migraine
(423894005)
Lower Half Migraine
(26150009)
Migraine (37796009)
Vascular Headache
(128187005)
Headache Disorder
(340461009)
Headache (25064002)
has_definitional_manifestation
Migraine (G43)
Migraine, unspecified
(G43.9)
Migraine, unspecified, not
intractable (G43.909)
Headache (R51)
Headache (748.0)
Other migraine (G43.8)
Lower half migraine
Cluster headache syndrome, unspecified
(G44.00)
synonymOf
excludes
Migraine (346)
Migraine, unspecified
(346.9)
54
![Page 55: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/55.jpg)
Refractory Migraine
(423894005)
Lower Half Migraine
(26150009)
Migraine (37796009)
Vascular Headache
(128187005)
Headache Disorder
(340461009)
Headache (25064002)
has_definitional_manifestation
Migraine (G43)
Migraine, unspecified
(G43.9)
Migraine, unspecified, not
intractable (G43.909)
Headache (R51)
Headache (748.0)
Other migraine (G43.8)
Lower half migraine
Cluster headache syndrome, unspecified
(G44.00)
synonymOf
excludes
Migraine (346)
Migraine, unspecified
(346.9)
55
![Page 56: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/56.jpg)
Refractory Migraine
(423894005)
Lower Half Migraine
(26150009)
Migraine (37796009)
Vascular Headache
(128187005)
Headache Disorder
(340461009)
Headache (25064002)
has_definitional_manifestation
Migraine (G43)
Migraine, unspecified
(G43.9)
Migraine, unspecified, not
intractable (G43.909)
Headache (R51)
Headache (748.0)
Other migraine (G43.8)
Lower half migraine
Cluster headache syndrome, unspecified
(G44.00)
synonymOf
excludes
Migraine (346)
Migraine, unspecified
(346.9)
ICD-10 excludes Lower Half Migraine from Migraine, but SNOMED still includes it.
Have a migraine?
56
![Page 57: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/57.jpg)
Data Warehousing with Semantic Ontologies
• Inclusion and mapping of BFO, IAO, OBI, and OGMS ontologies
• Inclusion and mapping of additional domain ontologies of interest
• Continuous analysis of SKOS consistency and compliance
• Tailoring of query layer to incorporate governance-approved semantic mappings and exceptions
57
![Page 58: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/58.jpg)
Mapping to STEPS™
http://www.himss.org/ValueSuite
We ended up here!
We ended up here!
58
![Page 59: Data Warehousing with Semantic Ontologiesrdcms-himss.s3.amazonaws.com/files/production/public/2015... · Fundamentals of Data Warehousing in Healthcare . 2013 HIMSS Annual Conference,](https://reader031.vdocuments.us/reader031/viewer/2022030417/5aa3e6d27f8b9ab4208ed2d2/html5/thumbnails/59.jpg)
Questions You are welcome to contact me
with questions at any time: • Richard E. Biehl, Ph.D.
Data-Oriented Quality Solutions
• LinkedIN: rbiehl
• Twitter: rbiehl
59