Quasi-Relational Query Language For Persistent Standardized EHRs Using no-SQL Databases

to Advance Knowledge for Humanity
Quasi-Relational Query Language

for Persistent Standardized EHRs:
Using No-SQL Databases
Aastha Madaan, W. Chu, Y. Daigo, S. Bhalla

University of Aizu
3/25/2013
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Introduction
EHRs Big data
Lifetime data temporal nature
Epidemic Query Needs (research on population) Big Data
Need Scalable and standardized ICT infrastructure

Data-standards EHRs HL7, CEN 13606, OpenEHR
Aim Knowledge-level interoperability
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Introduction (2)
Single-patient
Encounter
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OpenEHR Archetype
Concept: Blood Pressure (Example)
Maximal Definition : may be further revised

Currently: 352 archetype definitions
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Universal Schema: Archetypal Serialization

Archetype Definition Language (ADL)
XML variant, Complex structure
Uses Standard terminology codes (LOINC, SNOMED-CT, ICD)
definition
OBSERVATION[at0000] matches {
-- Blood Pressure
data matches {
HISTORY[at0001] matches { -- history
events cardinality matches {1..*; unordered} matches {
EVENT[at0006] occurrences matches {0..*} matches {
-- any event
data matches {
ITEM_TREE[at0003] matches { -- blood pressure
items cardinality matches {0..*; unordered} matches {
ELEMENT[at0004] occurrences matches {0..1} matches {-- Systolic
value matches {
C_DV_QUANTITY <
property = <[openehr::125]>
list = <
["1"] = <
Units = <"mm[Hg]">
magnitude = <|0.0..<1000.0|>
precision = <|0|>
>
>
>
}
}
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Query Options: AQL

AQL Archetype Query Language
Independent System environment, storage model
Developer level SQL +XQuery
An Example Find all the patients with high blood pressure values (Systolic
>= 140 AND Diastolic >= 90).
AQL Equivalent:
SELECT obs/data[at0001]/events[at0006]/data[at0003]/items[at0004]/value/magnitude,
obs/data[at0001]/events[at0006]/data[at0003]/items[at0005]/value/magnitude
FROM EHR [ehr_id/value=$ehrUid]
CONTAINS COMPOSITION c[openEHR-EHR-COMPOSITION.encounter.v1]
CONTAINS OBSERVATION obs[openEHR-EHR-OBSERVATION.blood_pressure.v1]
WHERE
obs/data[at0001]/events[at0006]/data[at0003]/items[at0004]/value/magnitude>=140
ANDobs/data[at0001]/events[at0006]/data[at0003]/items[at0005]/value/magnitude>=90
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Data Management Model

CODASYL Data Model v/s OpenEHR Data Management Model
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Archetypal EHRs: Database Options

Former Database Solutions
XML DB
Object DB
Relational DB
Object-Relational DB
Test prototype (Key-value store) Physical Layer

Cloud-based Database
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Conceptual View & New Query Language
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Problems
Universal Schema Interoperable across
distributed healthcare systems
Research focus:
Scalable persistence mechanism
New Query Language
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Context of Study
Traditional View
Input: Patient id
Target: Patients EHR
Need: Precise Information
Healthcare
worker
Modern View
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Standardized EHRs Database System
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The Proposal
1. Archetypal Definition Flattened Forms

2. QBE-style I/P & O/P Archetypal Definition
Possible to Query
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The Architecture
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Standardized EHRs Database Architecture (1)

Main Components
Local Archetype
Repository
Cloud-based
User-Interface
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Persistence
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Experimental Prototype
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Standardized EHRs Database Architecture(3)

NoSQL-based Persistence
ADL
Archetype
JSON document
Cloud-based
Persistence
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Unique id
Patient id
Version id
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Quasi-Relational Query Language

Archetypal QBE (AQBE)
Data Insert
Query UI
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Query Language Options

1. Continue with AQL ADL Store
2. AQBE Relational Store (PostgreSQL)
3. AQBE JSON Store (Cloud-DB)
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Quasi-Relational Query Language: AQBE
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The AQBE Data Insert

An Example
Store a patients blood pressure observation details
Insert the following details:
1. Patient Name: John_Barak
2. Composed By: Dr. Madaan
3. Systolic BP: 95
4. Diastolic BP: 150
AQBE-Data Insert UI
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Query-Requirements
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S. No.
Query Requirement
Population-based Queries
Single-patient Queries
Epidemiological Queries
Single-concept Queries
Multi-concept Queries
Temporal Queries
6(a)
Lifelong Queries
6(b)
Instantaneous Queries
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Demo: The AQBE Query Language (3)

Q3: [Single- patient, single-concept]
-Get a patients medication list
- Select Medication list concept
- Add patient name
- Find data
AQBE-Query UI
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Q1: [Single-concept, multiple EHRs]
-Get all the patients recorded with abnormal (high) BP values
during patient care
-
Select Blood pressure concept

Add Systolic > 140
Add Diastolic > 90
Find data
AQBE-Query UI
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Q2: [Single-concept , multiple patients]
-Find all the records with very high BMI value (>30) for patients
between the period of November 25, 2012 to January 21, 2013,
showing the sudden increase in obesity.
-
Select BMI concept

Add context value >= November 25, 2012
Add context value <= January 21, 2013
Enter BMI value > 30
Find Data
AQBE-Query UI
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Sample Set of Queries (1)

Current set of Queries
1.Get a patient's current medication list. [single-(concept/patient), projection]
2.Find high blood pressure values (systolic >= 140 or diastolic >= 90 ) within a
specified EHR.[single-(concept/patient), restrict & project]
3.Find high blood pressure values (systolic >= 140 and diastolic >= 90 ) within a
specified EHR. [single-(concept/patient), restrict & project]
4.Find blood pressure values where systolic/diastolic value >0.2 within a specified EHR.
[single-(concept/patient), divide]
5.Get BMI values > 30 kg/m2 for a specific patient. [single-(concept/patient), restrict &
project]
6.Get all HbA1c observations that have been done in the last 12 months for a specific
patient. [single-(concept/patient), restrict & project]
7.Find all blood pressure (BP) values for a specific patient, showing their systolic and
diastolic blood pressure values; also change the tag-name of systolic BP as 'Sys' and
Diastolic BP as 'Dias'. [single-(concept/patient), rename]
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8.
9.
10.
11.
12.
13.
14.
15.
Return all blood pressure (BP) elements having a position in which BP was record.
[single-(concept/patient), exists]
Get the blood pressure (BP)values where the position is not standing. [single(concept/patient), negation]
Find all the patients who have the same admitting doctor as 'A001'. [singleconcept, multi-patient,restrict & project]
Find all the patients who have diabetes but no record of hypertension
diagnosis.[XML definition not found]
Get the number of patients admitted on 9 October, 2012.[single-concept, multipatient, aggregate] <partial execution>
Get the number of all the patients with diabetes. .[XML definition not found]
Retrieve all patients who have not been discharged.[single-concept, multi-patient,
nested]
Get all patients who are suffering from the same problem as a specific patient (e.g.,
diagnosis is Diabetes). [single-concept, multi-patient, nested]
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Test Query Set Recent Literature Survey
16.The children of women which had medication XYZ during their first pregnancy
[complex query-multiple patients/concepts] (src: [11]).
17.Find the number of patients who were given medications during hospital course that
have caused an allergy in 1 or more patients[complex query- multiple patients/concepts,
aggregate, epidemiological] (src: [11]).
18.How many patients have had past medical history of anemia. patients[complex
query- multiple patients/concepts, aggregate, epidemiological] (src: [11]).
19.How many patients developed alopecia as a side effect of chemotherapy in the target
population[complex query- multiple patients/concepts, aggregate, epidemiological] (src:
[11]).
20.How many cases of small cell lung cancer are noted among smoking females in the
target population. [complex query- multiple patients/concepts, aggregate,
epidemiological] (src: [11]).
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22.
23.
24.
To retrieve results containing 3 concepts (Fever, sore throat, and cough

with 1 concept having 2 sub-keys with numerical value (Temp > 38.2 deg and
duration > 1 day) [complex query- multiple patients/concepts](src: [36]).
To retrieve results containing 5 concepts (fever, sore throat, cough, no
vomiting and sputum);2 concepts having 1 sub-key with numerical value
(fever temp > 38.2 deg and duration > 1day) and 1 concept having 1 sub-key with
textual value (i.e. sputum of yellow color). [complex query- multiple
patients/concepts](src: [36]).
To retrieve results containing 3 clinical concepts (cough, no sore-throat, and
had no sterol injection) with 1 concept having 1 sub-key with textual value (i.e.
non sterol injection at the left side). [complex query- multiple
patients/concepts](src: [36]).
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AQBE Query Language (2)

S. No.
Query Requirement
AQBE Query Language Capability
Population-based Queries
Yes
Single-patient Queries
Yes
Epidemiological Queries
Single-concept Queries
Yes
Multi-concept Queries
Challenge
Temporal Queries
Yes
6(a)
Lifelong Queries
Challenge
6(b)
Instantaneous Queries
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Challenge
Yes
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AQBE Query Language (3)

Query Function Support
Query Type
Simple Query(Select)
AQL [5]
(Ocean
Informatics)
AQBE [30]
(Relational
DB)
AQBE
(NoSQL DB)
(Except Distinct
To be explored
To be explored
To be explored
To be explored
To be explored
Filtered Query(Where Clause)

Sorted Query(Order By)
Grouping, Summary and Analysis(Group By,
Having, grouping/ aggregation/ analytical
functions)
Joins and Intersection(Outer/Inner/
Natural/Range/Equi/Self)
Sub-query (In/Not In/Nested/
Parallel/Multi(row/column)/single row)
Hierarchical Query
Composite Query(Union, Union All,
Intersect, Minus)
To be explored
Top-N Query
To be explored
To be explored
To be explored
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To be explored To be explored
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Persistence Method Comparison

PostgreSQL
(Relational DB) [35]
Feature
Scalability
Single large relation
Versioning is expensive
Performance Relational queries slow [1]
like AQL (limited

Queryability SQL
capability)
Indexing
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MongoDB
Document-Oriented
(No-SQL DB)
DB XML(Berkeley)
(XML DB) [28]
Limited scalability
Nested structure
archetypes and
templates
Each concept stored JSON

document (unique id and
version id)
Limited query response
Light application
Each node traversed
Fast query-response
Epidemiological queries
Low performance
Proposed AQBE language

potential powerful querying
Automatic
Database pre-defined
Automatic
Composite/secondary
indexing
May not be suitable
Composite/secondary
indexing
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Further Challenges
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1. Temporal Complexity
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Current Task
Upgrade existing Query Language
Implement More algebraic operations
Similar to SQL with simplified User-interface
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Summary and Conclusions

New Quasi-Relational Query Language
A. Possibility Cloud-based, scalable persistence for archetypal EHRs

B. Ease of query healthcare users
C. Facilitate Complex Queries for developers
D. Reduce Dependency on commercial query tools
E. Facilitate Creation of new SEHR database
Capable to exchange data with MS Health Vault and Google Health
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References (1)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
Jacobs, A.: Pathologies of Big Data. Communications of ACM 52(8) (August 2009)
ADL for archetypes downloaded, http://www.openehr.org/svn/knowledge/archetypes/dev/html/
index_en.html
Any+time date picker downloaded form, http://www.ama3.com/anytime/
AQL query builder available at, http://www.oceaninformatics.com/
Solutions/openehr-solutions/ocean-products/Clinical-Modelling/Ocean-Query-Builder.html
Archetype Query Language, http://www.openehr.org/wiki/display/spec/~Archetype+Query+Language+Description
Beale, T., Heard, S., Kalra, D., Llyod, D.: The OpenEHR Reference Model: EHR Information Model, The
OpenEHR release 1.0.2., OpenEHR Foundation (2008)
Beale, T.: The OpenEHR Archetype Model-Archetype Object Model, The OpenEHR release 1.0.2., OpenEHR
Foundation (2008)
Casbah plugin available at, https://github.com/mongodb/casbah
CEN 13606 standard, http://www.en13606.org/the-ceniso-en13606-standard
Clinical Knowledge Manager, http://www.openehr.org/knowledge/
Eclipse 4.2.0, http://www.eclipse.org/
Redmond, E., Wilson, J.R.: Book: Seven Databases in Seven Weeks (May 2012)
HTML 5, http://www.w3schools.com/html/html5_intro.asp
http://wako3.u-aizu.ac.jp:8080/aqbe/
ISO 13606-1: Health informatics - Electronic health record communication- Part 1: RM., 1st edn. (2008)
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References (2)
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
JavaScript, http://www.w3schools.com/js/default.asp
jQuery downloaded from, http://jquery.com/
jQuery UI available at, http://jqueryui.com/
Lift JSON available at, https://github.com/lift/lift/tree/master/framework/lift-base/lift-json/
MongoDB available at, http://www.mongodb.org/
Zloof, M.M.: Query-By-Example: The invocation and definition of tables and forms (1975)
Opereffa Project available at, http://www.openehr.org/wiki/display/projects/Opereffa+Project
Play framework available at, http://www.playframework.org/
PostgreSQL database downloadable from, http://www.postgresql.org/
Scala Plugin available at, http://www.scala-lang.org/
Freire, S.M., Sundvall, E., Karlsson, D., Lambrix, P.: Performance of XML Databases for Epidemiological Queries
in Archetype-Based EHRs. In: Scandinavian Conference on Health Informatics 2012, Linkping, Sweden, October
23 (2012)
29. Sachdeva, S., Madaan, A., Chu, W.: Information interchange services for electronic health record databases. IJCSE
7(1), 3851 (2012)
30. Sachdeva, S., Yaginuma, D., Chu, W., Bhalla, S.: AQBE - QBE Style Queries for Archetyped Data. IEICE
Transactions 95-D(3), 861871 (2012)
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References (3)
31. Sachdeva, S., Bhalla, S.: Semantic interoperability in standardized electronic health record databases. J. Data
and Information Quality 3(1), 1 (2012)
32. Beale, T.: OpenEHR: Node + Path Persistence (2008)
33. Twitter bootstrap framework downloaded from, http://twitter.github.com/bootstrap/
34. http://www.linkedin.com/groups/Choice-OpenEHR-persistence-layer-144276.S.208531138?qid=208adbcafc26-4ada-bf02-7efe5a9e5661&trk=group_most_recent_rich-0-b-ttl&goback=%2Egmr_144276
35. http://www.openehr.org/wiki/display/projects/Opereffa+Project
36. Ken Ka-Yin Lee, Wai-Choi Tang, Kup-Sze Choi, Alternatives to relational database: Comparison of NoSQL
and XML approaches for clinical data storage, Computer Methods and Programs in Biomedicine, Volume
110, Issue 1, April 2013, Pages 99109
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Questions
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