a quasi relational query language for persistent standardized ehrs: using nosql databases
TRANSCRIPT
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Aastha Madaan, W. Chu, Y. Daigo, S. Bhalla
University of Aizu
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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
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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 Introduction
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Single-patient Encounter
Introduction (2)Introduction (2)
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OpenEHR ArchetypeOpenEHR Archetype
Maximal Definition : may be further revised
Currently: 352 archetype definitions
Concept: Blood Pressure (Example)
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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|>>>
>}
}
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Archetype Definition Language (ADL) XML variant, Complex structure Uses → Standard terminology codes (LOINC, SNOMED-CT, ICD)
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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
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Data Management ModelData Management Model CODASYL Data Model v/s OpenEHR Data Management Model
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Former Database Solutions
Test prototype (Key-value store) → Physical Layer
Cloud-based Database
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Archetypal EHRs: Database OptionsArchetypal EHRs: Database Options
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XML DB
Relational DB
Object DB
Object-Relational DB
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Conceptual View & New Query LanguageConceptual View & New Query Language
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ProblemsProblems
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Universal Schema → Interoperable across distributed healthcare systems
Research focus:Scalable persistence mechanism
New Query Language →
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Context of StudyContext of Study
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Healthcare worker
Input: Patient id
Target: Patient’s EHR
Need: Precise Information
Modern View
Traditional View
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Standardized EHRs Database System
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The ProposalThe 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)Standardized EHRs Database Architecture (1)
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Main Components
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Local Archetype
Repository
Cloud-based
PersistenceUser-Interface
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Experimental PrototypeExperimental Prototype
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Standardized EHRs Database Architecture(3)Standardized EHRs Database Architecture(3)
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NoSQL-based Persistence
JSON document
Archetype
Cloud-based
Persistence
• Unique id• Patient id• Version id
ADL
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Quasi-Relational Query Language
Archetypal QBE (AQBE)Data InsertQuery UI
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Query Language OptionsQuery 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 InsertThe AQBE – Data Insert
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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
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Query-RequirementsQuery-Requirements
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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
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Demo:Demo: The AQBE –Query Language (3)The AQBE –Query Language (3)
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Q3: [Single- patient, single-concept]
-Get a patient’s medication list
- Select → Medication list concept- Add → patient name- Find data
AQBE-Query UI
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Demo:Demo: The AQBE –Query Language (1)The AQBE –Query Language (1)
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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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Demo:Demo: The AQBE –Query Language (2)The AQBE –Query Language (2)
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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)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. 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]
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Sample Set of Queries (2)Sample Set of Queries (2)
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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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Sample Set of Queries (3)Sample Set of Queries (3)
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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]).
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Sample Set of Queries (4)Sample Set of Queries (4)
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AQBE Query Language (2)AQBE Query Language (2)
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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
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AQBE Query Language (3)AQBE Query Language (3) Query Function Support
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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
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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
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Further Challenges
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1. Temporal Complexity 1. Temporal Complexity
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Current TaskCurrent Task
Upgrade existing Query Language
Implement → More algebraic operations
Similar to SQL with simplified User-interface
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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
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References (1)References (1)
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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)
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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)
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References (2)References (2)
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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
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