A Quasi Relational Query Language for Persistent Standardized EHRs: Using NoSQL Databases

to Advance Knowledge for Humanityto Advance Knowledge for Humanity

Aastha Madaan, W. Chu, Y. Daigo, S. Bhalla

University of Aizu

1

Quasi-Relational Query LanguageQuasi-Relational Query Languagefor Persistent Standardized EHRs:for Persistent Standardized EHRs:

Using No-SQL DatabasesUsing No-SQL Databases

05/01/23 DNIS 2013


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

05/01/23 2DNIS 2013

Introduction Introduction


05/01/23 3DNIS 2013

Single-patient Encounter

Introduction (2)Introduction (2)


405/01/23 DNIS 2013

OpenEHR ArchetypeOpenEHR Archetype

Maximal Definition : may be further revised

Currently: 352 archetype definitions

Concept: Blood Pressure (Example)


Universal Schema: Archetypal SerializationUniversal Schema: Archetypal Serialization

definitionOBSERVATION[at0000] matches { -- Blood Pressure

data matches {HISTORY[at0001] matches { -- history

events cardinality matches {1..*; unordered} matches {EVENT[at0006] occurrences matches {0..*} matches { -- any eventdata matches {ITEM_TREE[at0003] matches {-- blood pressure

items cardinality matches {0..*; unordered} matches {ELEMENT[at0004] occurrences matches {0..1} matches {-- Systolicvalue matches {C_DV_QUANTITY <

property = <[openehr::125]>list = <["1"] = <Units = <"mm[Hg]">magnitude = <|0.0..<1000.0|>precision = <|0|>>>

>}

}

05/01/23 DNIS 2013 5

Archetype Definition Language (ADL) XML variant, Complex structure Uses → Standard terminology codes (LOINC, SNOMED-CT, ICD)


QueryQuery Options: AQLOptions: 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]WHEREobs/data[at0001]/events[at0006]/data[at0003]/items[at0004]/value/magnitude>=140ANDobs/data[at0001]/events[at0006]/data[at0003]/items[at0005]/value/magnitude>=90

05/01/23 DNIS 2013 6


Data Management ModelData Management Model CODASYL Data Model v/s OpenEHR Data Management Model

05/01/23 7DNIS 2013


Former Database Solutions

Test prototype (Key-value store) → Physical Layer

Cloud-based Database

05/01/23 8

Archetypal EHRs: Database OptionsArchetypal EHRs: Database Options

DNIS 2013

XML DB

Relational DB

Object DB

Object-Relational DB


Conceptual View & New Query LanguageConceptual View & New Query Language

05/01/23 DNIS 2013 9


ProblemsProblems

1005/01/23

Universal Schema → Interoperable across distributed healthcare systems

Research focus:Scalable persistence mechanism

New Query Language →

DNIS 2013


Context of StudyContext of Study

05/01/23 DNIS 2013 11

Healthcare worker

Input: Patient id

Target: Patient’s EHR

Need: Precise Information

Modern View

Traditional View


1205/01/23

Standardized EHRs Database System

DNIS 2013


05/01/23 DNIS 2013 13

The ProposalThe Proposal

1. Archetypal Definition → Flattened Forms

2. QBE-style I/P & O/P→ Archetypal Definition

Possible to Query


1405/01/23

The Architecture

DNIS 2013


Standardized EHRs Database Architecture (1)Standardized EHRs Database Architecture (1)

1505/01/23

Main Components

DNIS 2013

Local Archetype

Repository

Cloud-based

PersistenceUser-Interface


Experimental PrototypeExperimental Prototype

05/01/23 16DNIS 2013


05/01/23 17

Standardized EHRs Database Architecture(3)Standardized EHRs Database Architecture(3)

DNIS 2013

NoSQL-based Persistence

JSON document

Archetype

Cloud-based

Persistence

• Unique id• Patient id• Version id

ADL


1805/01/23

Quasi-Relational Query Language

Archetypal QBE (AQBE)Data InsertQuery UI

DNIS 2013


Query Language OptionsQuery Language Options

1. Continue with AQL → ADL Store

2. AQBE → Relational Store (PostgreSQL)

3. AQBE → JSON Store (Cloud-DB)

05/01/23 DNIS 2013 19


2005/01/23

Quasi-Relational Query Language: AQBE

DNIS 2013


The AQBE – Data InsertThe AQBE – Data Insert

2105/01/23 DNIS 2013

An ExampleStore a patient’s blood pressure observation details

Insert the following details:1. Patient Name: John_Barak2. Composed By: Dr. Madaan3. Systolic BP: 954. Diastolic BP: 150

AQBE-Data Insert UI


Query-RequirementsQuery-Requirements

05/01/23 DNIS 2013 22

S. No. Query Requirement1 Population-based Queries

2 Single-patient Queries

3 Epidemiological Queries

4 Single-concept Queries

5 Multi-concept Queries

6 Temporal Queries

6(a) Lifelong Queries

6(b) Instantaneous Queries


Demo:Demo: The AQBE –Query Language (3)The AQBE –Query Language (3)

2305/01/23

Q3: [Single- patient, single-concept]

-Get a patient’s medication list

- Select → Medication list concept- Add → patient name- Find data

AQBE-Query UI

DNIS 2013



2405/01/23

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

DNIS 2013



2505/01/23

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

DNIS 2013


Sample Set of Queries (1)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]

05/01/23 DNIS 2013 26


8. Return all blood pressure (BP) elements having a position in which BP was record. [single-(concept/patient), exists]

9. Get the blood pressure (BP)values where the position is not standing. [single-(concept/patient), negation]

10. Find all the patients who have the same admitting doctor as 'A001'. [single-concept, multi-patient,restrict & project]

11. Find all the patients who have diabetes but no record of hypertension diagnosis.[XML definition not found]

12. Get the number of patients admitted on 9 October, 2012.[single-concept, multi-patient, aggregate] <partial execution>

13. Get the number of all the patients with diabetes. .[XML definition not found]14. Retrieve all patients who have not been discharged.[single-concept, multi-patient,

nested]15. Get all patients who are suffering from the same problem as a specific patient

(e.g., diagnosis is ‘Diabetes’). [single-concept, multi-patient, nested]

05/01/23 DNIS 2013 27

Sample Set of Queries (2)Sample Set of Queries (2)


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]).

05/01/23 DNIS 2013 28



22. 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]).

23. 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]).

24. 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]).

05/01/23 DNIS 2013 29



AQBE Query Language (2)AQBE Query Language (2)

3005/01/23 DNIS 2013

S. No. Query Requirement AQBE Query Language Capability1 Population-based Queries Yes

2 Single-patient Queries Yes

3 Epidemiological Queries Challenge

4 Single-concept Queries Yes

5 Multi-concept Queries Challenge

6 Temporal Queries Yes

6(a) Lifelong Queries Challenge

6(b) Instantaneous Queries Yes


AQBE Query Language (3)AQBE Query Language (3) Query Function Support

3105/01/23

Query TypeAQL [5](Ocean

Informatics)AQBE [30](Relational

DB)AQBE

(NoSQL DB)

Simple Query(Select)

Filtered Query(Where Clause)

Sorted Query(Order By) (Except Distinct Grouping, Summary and Analysis(Group By, Having, grouping/ aggregation/ analytical functions)

To be explored To be explored

Joins and Intersection(Outer/Inner/ Natural/Range/Equi/Self) To be explored

Sub-query (In/Not In/Nested/ Parallel/Multi(row/column)/single row) To be explored To be explored

Hierarchical Query To be explored To be explored To be explored Composite Query(Union, Union All, Intersect, Minus)

Top-N Query To be explored To be explored To be explored

DNIS 2013


05/01/23 32

Persistence Method ComparisonPersistence Method ComparisonFeature PostgreSQL

(Relational DB) [35]DB XML(Berkeley)

(XML DB) [28]MongoDB

Document-Oriented (No-SQL DB)

Scalability• Single large relation

• Versioning is expensive

• Limited scalability

• Nested structure → archetypes and templates

Each concept stored →JSON document (unique id and version id)

Performance Relational queries slow [1]Limited query response – Each node traversed

• Light application

• Fast query-response

Queryability SQL like AQL (limited capability)

Epidemiological queries → Low performance

Proposed AQBE language potential → powerful querying

Indexing• Automatic

• Composite/secondary indexing

• Database pre-defined

• May not be suitable

• Automatic

• Composite/secondary indexing

DNIS 2013


3305/01/23

Further Challenges

DNIS 2013


3405/01/23

1. Temporal Complexity 1. Temporal Complexity

DNIS 2013


Current TaskCurrent Task

Upgrade existing Query Language

Implement → More algebraic operations

Similar to SQL with simplified User-interface

05/01/23 DNIS 2013 35


Summary and Conclusions 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

3605/01/23 DNIS 2013


References (1)References (1)

3705/01/23

1. Jacobs, A.: Pathologies of Big Data. Communications of ACM 52(8) (August 2009)2. ADL for archetypes downloaded, http://www.openehr.org/svn/knowledge/archetypes/dev/html/3. index_en.html4. Any+time date picker downloaded form, http://www.ama3.com/anytime/5. AQL query builder available at, http://www.oceaninformatics.com/6. Solutions/openehr-solutions/ocean-products/Clinical-Modelling/Ocean-Query-Builder.html7. Archetype Query Language, http://www.openehr.org/wiki/display/spec/~Archetype+Query+Language+Description8. Beale, T., Heard, S., Kalra, D., Llyod, D.: The OpenEHR Reference Model: EHR Information Model, The OpenEHR release

1.0.2., OpenEHR Foundation (2008)9. Beale, T.: The OpenEHR Archetype Model-Archetype Object Model, The OpenEHR release 1.0.2., OpenEHR Foundation

(2008)10. Casbah plugin available at, https://github.com/mongodb/casbah11. CEN 13606 standard, http://www.en13606.org/the-ceniso-en13606-standard12. Clinical Knowledge Manager, http://www.openehr.org/knowledge/13. Eclipse 4.2.0, http://www.eclipse.org/14. Redmond, E., Wilson, J.R.: Book: Seven Databases in Seven Weeks (May 2012)15. HTML 5, http://www.w3schools.com/html/html5_intro.asp16. http://wako3.u-aizu.ac.jp:8080/aqbe/17. ISO 13606-1: Health informatics - Electronic health record communication- Part 1: RM., 1st edn. (2008)

DNIS 2013


18. JavaScript, http://www.w3schools.com/js/default.asp19. jQuery downloaded from, http://jquery.com/20. jQuery UI available at, http://jqueryui.com/21. Lift JSON available at, https://github.com/lift/lift/tree/master/framework/lift-base/lift-json/22. MongoDB available at, http://www.mongodb.org/23. Zloof, M.M.: Query-By-Example: The invocation and definition of tables and forms (1975)24. Opereffa Project available at, http://www.openehr.org/wiki/display/projects/Opereffa+Project25. Play framework available at, http://www.playframework.org/26. PostgreSQL database downloadable from, http://www.postgresql.org/27. Scala Plugin available at, http://www.scala-lang.org/28. 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, Linköping, Sweden, October 2–3 (2012)

29. Sachdeva, S., Madaan, A., Chu, W.: Information interchange services for electronic health record databases. IJCSE 7(1), 38–51 (2012)

30. Sachdeva, S., Yaginuma, D., Chu, W., Bhalla, S.: AQBE - QBE Style Queries for Archetyped Data. IEICE Transactions 95-D(3), 861–871 (2012)

05/01/23 DNIS 2013 38



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=208adbca-

fc26-4ada-bf02-7efe5a9e5661&trk=group_most_recent_rich-0-b-ttl&goback=%2Egmr_14427635. http://www.openehr.org/wiki/display/projects/Opereffa+Project36. 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 99–109

05/01/23 DNIS 2013 39



QuestionsQuestions

4005/01/23 DNIS 2013

Date post:	09-Feb-2017
Category:	Health & Medicine
Upload:	aastha-madaan
View:	181 times
Download:	1 times

A Quasi Relational Query Language for Persistent Standardized EHRs: Using NoSQL Databases

Health & Medicine