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Object Databases and Object Persistence Framework for openEHR Student: Travis Muirhead Supervisor: Jan Stanek Associate Supervisors: Chunlan Ma Heath Frankel.

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Presentation on theme: "Object Databases and Object Persistence Framework for openEHR Student: Travis Muirhead Supervisor: Jan Stanek Associate Supervisors: Chunlan Ma Heath Frankel."— Presentation transcript:

1 Object Databases and Object Persistence Framework for openEHR Student: Travis Muirhead Supervisor: Jan Stanek Associate Supervisors: Chunlan Ma Heath Frankel

2 2 Overview Background openEHR foundation and architecture Motivation Structural and Semantic Issues relating to openEHR systems Performance Issues in XML and Relational databases storing complex object structures Preliminary Evaluation Linear recursion test OODB product comparison Final Evaluation Real test data and common queries Scope and bounds Conclusion

3 openEHR foundation Non-profit organisation Produces open specifications for Electronic Health Records Specifications address many challenges in EHR such as: Semantic Interoperability Continual Change and Complexity Maintainability 3

4 openEHR Architecture Separation of knowledge and information 4 Archetype Software Meta-Architecture. (Beale, Thomas 2002)

5 openEHR Architecture Two-Level Modelling Approach 5 A Two-Level Modelling Paradigm (Beale, Thomas 2002)

6 openEHR Architecture 6 Archetype Query Language Terminology Subset Syntax openEHR package structure (Beale, T & Heard, S 2007c) My scope: The Reference Model (RM)

7 openEHR Architecture 7 Complex Structure – The persistence problem Elements of an openEHR Composition (Beale, T & Heard, S 2007c)

8 openEHR Architecture 8 AQL (Path Based Querying) Navigational based, similar to XML query languages SELECT o/data[at0001]/events[at0006]/data[at0003]/items[at0004]/value AS Systolic, o/data[at0001]/events[at0006]/data[at0003]/items[at0005]/value AS Diastolic FROM EHR [ehr_id=$ehrUid] CONTAINS COMPOSITION c[openEHR-EHR-COMPOSITION.encounter.v1] CONTAINS OBSERVATION o[openEHR-EHR-OBSERVATION.blood_pressure.v1] WHERE o/data[at0001]/events[at0006]/data[at0003]/items[at0004]/value/value >= 140 OR o/data[at0001]/events[at0006]/data[at0003]/items[at0005]/value/value >= 90 A typical EQL query (Ma, C, Frankel, H, Beale, T & Heard, 2007)

9 Motivation for study Only known implementation of the persistence layer is in Microsoft SQL Server 2005 Hybrid XML / Relational Approach Extensive mappings Doesn’t use the native XML support Issues with the current approach Parsing XML is usually slow Smallest unit that can be retrieved is the top level container Even the native query approach has limitations For example: Querying facilities require improvement 9

10 What about pure relational databases? 10 Join Operations Slow especially for deep tree structures Can try flattening structures but this results in many NULL fields Difficult to join many tables and maintain semantics Example from the Objectivity white pages (Bioinformatics case study): Finding all the Amino Acids associated with a Protein

11 11 Alternative persistence solutions Object-Relational Mapping (ORM) Framework to map classes written in an OO language to Relational database Tables Object-Relational conversion adds overhead eg. Hibernate, TopLink Object-Relational Databases Additional OO features as layers to Relational Databases Data still resides in tables and tables are not generated by classes Eg. UniSQL, Oracle, Sybase

12 12 Alternative persistence solutions Object-Oriented Databases (OODB) Transparent Persistence No Impedance Mismatch Removes overhead of querying XML structures with the Relational approach using XML Blobs Removes overhead of complex joins on deep hierarchical structures Improves navigational access Handles recursive and deep hierarchical tree structures well Maps well to the openEHR specification eg. Caché, dbo4, Objectivity/db

13 13 Selection of OODB Products – Db4o Opportunities Transparent persistence API XTEA (eXtended Tiny Encryption Algorithm) fast, reasonably secure Lack of authentication and access control Small overhead – Ideal for mobile health care No Administration and schema evolution Tight integration with C# and Java Limitations: Query Scope Activation implementation Little support for high availability dRS replication service only form of distribution Manage your own pooling Optimal blocksize 8kb – Only 16GB maximum file size

14 14 Selection of OODB Products – Caché Opportunities Post-Relational (Multidimensional, Object and Relational views) Transparent distribution with ECP Implicit Locking Role-Based Access Control (RBAC) – similar to openEHR AES encryption Journal Roll Forward Clustering 24/7 Support Limitations: Only provides tight integration with Java Some mapping required Steeper learning curve

15 15 Selection of OODB Products– Objectivity/DB Objectivity for Java Programmer’s Guide (Objectivity, 2006)

16 16 Selection of OODB Products– Objectivity/DB Opportunities Tight Integration with many programming languages Very Scalable (BaBar system) Possible to have 4 times the amount of databases across a federation in comparison to Caché Parallel Queries Schema Evolution – A possibility to map ADL definitions to data structures Partitions – resource sharing, replication Limitations: Container level locking Little support for security features High availability package is a separate product Rollback journaling only

17 Preliminary Evaluation Linear Recursive Structure Testing Evaluate some aspects of openEHR structures in several databases Assist in identifying implementation and performance issues before settling on a database and implementing a complex domain model. Little success with using own structures for lookups in db4o Query scope was too course-grained for complex objects Forced to use id’s and db4o OID’s 17 HeadNode Long headID Node node; Long headID Long position Node next; 0.. * 0.. 1

18 Preliminary Evaluation 18 Bulk Insertion Time Insert 10,000 head objects containing 100 nodes each

19 Preliminary Evaluation 19 Insertion at Fixed Intervals Insert 10,000 head objects followed by 50 head objects (committing one at a time) and repeat 50 times

20 Preliminary Evaluation 20 Find Single Node (Non-Cached results) Find node at position #50 within a head object with hID = 2500

21 Preliminary Evaluation 21 Find Single Node (Cached Results) Find node at position #50 within a head object from hID = 2000 to hID =2999

22 Preliminary Evaluation 22 Find Group Node (Non-Cached Results) Find all nodes inside head objects with identifiers in between 2500 and 2500+gapsize. The test was performed with gap sizes: 5, 10, 20, 50, 100, 200 Further test showed traversal at node 1 resulted in ~ 6 ms average where as traversal to 99 resulted in 369 ms average Lookup for both resulted in ~ 4ms

23 Final Evaluation Implementation in Intersystems Caché Implement openEHRV1 in Caché and C# Better scalability than db4o Administrative characteristics of distribution over Objectivity/DB Availability of license Test Data Trying to obtain some real test data to use Evaluation Also finding statistics for most common database operations More specific than the preliminary evaluation Statistical Analysis 23

24 Conclusion Difficult to map openEHR architecture to a Relational Model. Hybrid XML approach limited OODBs provide a closer mapping and better performance due to references (particularly with path based queries) Development time is decreased Some of the most scalable systems use OODBMSs Final Evaluation will provide some insight into the performance aspects within a controlled environment Scope for future work in comparing distributed solutions 24

25 References Provided for figures: Beale, T 2002, Archetypes: Constraint-based Domain Models for Future-proof Information Systems. Beale, T & Heard, S 2007c, Architecture Overview, openEHR Foundation. Ma, C, Frankel, H, Beale, T & Heard, S 2007, 'EHR Query Language (EQL) - A Query Language for Archetype-Based Health Records', MEDINFO. Objectivity, I 2007, Whitepaper: Objectivity/DB in Bioinformatics Applications, Objectivity, California, p. 9. Objectivity, I 2006a, Objectivity for Java Programmer’s Guide Release 9.3, Objectivity, Sunnyvale. 25 See minor thesis for complete list

26 26 Questions?


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