to Advance Knowledge for Humanity to Advance Knowledge for Humanity Aastha Madaan , W. Chu, Y. Daigo, S. Bhalla University of Aizu 1 Quasi-Relational Query Language Quasi-Relational Query Language for Persistent Standardized EHRs: for Persistent Standardized EHRs: Using No-SQL Databases Using No-SQL Databases 03/02/22 DNIS 2013
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A Quasi Relational Query Language for Persistent Standardized EHRs: Using NoSQL Databases
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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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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
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)
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
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References (3)References (3)
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