An integrated. EHR system

Transcription

1 An integrated t Expression Repository EHR system Daniel Karlsson, Mikael Nyström, Bengt Kron

2 Project goals Develop and test a system for storing and querying pre- and post-coordinated SNOMED CT expressions in an Electronic Health Record (EHR) system SNOMED CT is used as a reference terminology SNOMED CT allows abstraction of EHR data for transfer to quality databases 2

3 3 Pre- and post-coordination

4 Pre-coordination: Pain Pain 4

5 Pre-coordination: Pain 31 children 787 decendents 5

6 Post-coordination: Pain, Severity Pain : Severity = Mild to moderate 6

7 7 Post-coordination: Pain, All 7 Severities

8 8 Post-coordination: Pain, all defining attributes Finding site, Pathological process, 3 Associated Has definitional morphology, manifestation, Causative agent, Occurrence, Finding method, Due to, Finding informer, 4 After, Severity, 7 5,5 * possibilities Clinical course, 31 Approximately Episodicity, 5 4,9 * sensible Interprets, possibilities Has interpretation, pre-coordinated decendents

9 Post-coordination: Pain after operation on neck 9

10 Post-coordination: Pain after operation on neck 10

11 Post-coordination: Recurrent disease of cardiovascular asc systemstem 11

12 Post-coordination: Recurrent disease of cardiovascular asc systemstem 12

13 Rationale for an expression repository Classifiers typically does not handle changes between releases and over time Each addition of a new post-coordinated expression creates a new version Unnecessary to classify each time an expression is submitted Classifications of equivalent expressions can be reused Expressions might contain more characters than current systems can handle Fully defined post-coordinated expressions decrease the maintenance cost compared to extensions with pre-coordinated concepts 13

14 Expression repository architecture EHR prototype t EEE XML DB Expression repository Data store OWL Classifier 14

15 Expression repository Classifier used to classify new post-coordinated expressions OWL API-compliant classifiers (Snorocket, ELK,...) SNOMED CT expressions are translated to OWL Result of classification fed to data store SNOMED CT query results aggregated from data store 15

16 Equivalent expressions Structural equivalent expressions are only stored once in the repository the equivalence can never be lost Semantic, but not structural, equivalent expressions are stored individually are linked to each other have shared rows in the transitive closure table the equivalence might be lost due to updates in new releases Disorder of intestine : { Finding site = Appendix structure, Associated morphology = Inflammation } Disorder of intestine : { Associated morphology = Inflammation, Finding site = Appendix structure } Structural eq Semantic eq Inflammatory disorder : d { Finding site = Appendix structure } 16

17 Expression repository flow Expression submitted Parsing, syntactic normalizing New expression? No Return id Yes Build OWL expression Classify Store Return new id 17

18 Expression repository: Data store Data stored in tables in the relational database PostgreSQL Communicate through h a Java class Contains a full release Manages the expression s history Data storage and retrieval methods include Store an expression Store equivalence among expressions Store parents and children to an expression Get an expression s parents Get an expression s ancestors Get an expression s children Get an expression s descendants 18

19 Expression repository: Data store Transitive closure table Source Destination Start End Direct Yes Yes No No Current international full release gives rows 19

20 Differences to Technical Implementation Guide Uses a full release Manages the expression s history Uses a classifier Do not store the normal form 20

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