1. C LIENT R EGISTRY OpenEMPI: Operations Support Training SYSNET International, Inc.

2. OpenEMPI Software Stack Database Server: PostgreSQL open source database, version 9.1 Application Server: JBoss version 4.2.3 Web Server: Apache HTTP Server, version 2.4

3. Overview of Operational Support Tasks Starting the Application Server Stopping the Application Server Starting the Database Server Stopping the Database Server Changing database account passwords Managing OpenEMPI user accounts Back-up the application software Back-up the Client Registry data Viewing log files Monitor the server load

4. Starting the Application Server JBoss Installation Directory /home/sysnet/servers/jboss-4.2.3 Setting the environment $ source /home/sysnet/openempi/openempi_env.sh Start the server $ cd /home/sysnet/servers/jboss-4.2.3 $ bin/run.sh

5. Server’s Memory Configuration Will be configured appropriately but if necessary, adjustments can be made over time In bin/run.conf JAVA_OPTS="-Xms128m -Xmx2048m -XX:MaxPermSize=512m … -Xms:Sets the starting heap size -Xmx: Sets the maximum heap size -XX:MaxPermSize:Sets the size of the memory allocated to storing class information

6. Stopping the Application Server JBoss Installation Directory /home/sysnet/servers/jboss-4.2.3 Setting the environment $ source /home/sysnet/openempi/openempi_env.sh Start the server $ cd /home/sysnet/servers/jboss-4.2.3 $ bin/shutdown.sh --shutdown

7. Starting/Stopping the Database Server PostgreSQL 9.1 installed as Unix service Starting the server: $ sudo /etc/init.d/posgresql start Stopping the server: $ sudo /etc/init.d/posgresql stop

8. Database Accounts Account postgres is privileged; it is created when the software is installed Account openempi is created during installation of OpenEMPI To change the openempi password, first connect to Postgres server with client application psql --username=openempi --host=localhost openempi

9. Change Database Password Once connected, use the alter user command: ALTER USER openempi WITH PASSWORD ‘xxxxxxxxx'; Note: ‘xxxxxxxxx’ is just a placeholder for the password; so a strong password Must tell OpenEMPI that database password has changed $ cd /home/sysnet/openempi/conf $ vi jdbc.properties jdbc.username=openempi jdbc.password=openempi

10. Managing OpenEMPI Accounts Use the security tab to manage accounts and privileges

11. Manage Roles From the Security tab select Manager Roles

12. Manage Roles Roles have one or more permissions assigned to them.

13. Backup Database Postgres includes the pg_dump tool for backups pg_dump --username=openempi --password \ --host=localhost openempi gzip \ /home/sysnet/backups/openempi-db-backup-mm-dd-yyyy.sql.gz Software backs up everything within the database A script will be developed to automate this process Backups should be done on a daily basis

14. Backup Software All the software that needs to be preserved resides under: /home/sysnet Filesystem backups may be performed at the virtual machine level Backup strategy will be refined once the server hosting the client registry is made available to us

15. Log Files The primary log file for the Client Registry is: /home/sysnet/openempi/openempi.log Stores operational information at a configurable log level /home/sysnet/openempi/conf/log4j.properties log4j.rootCategory=warn, R, O Log level takes the values below (increasing detail): error, warn, info, debug, trace Application server’s log file: /home/sysnet/servers/jboss-4.2.3.GA/server/default/log/server.log

16. System Monitoring It is useful to periodically monitor the performance of the server vmstat 5 (sar is another alternative) procs -----------memory---------- ---swap-- -----io---- -system-- ----cpu---- r b swpd free buff cache si so bi bo in cs us sy id wa 1 0 769136 166932 21272 2298044 1 1 21 18 3 1 2 2 95 0 4 0 769136 165664 21280 2298392 0 0 1 20 4833 17126 5 11 83 0 0 0 769136 164272 21288 2298392 0 0 0 14 4870 18597 6 12 82 0 You want to verify: System has plenty of memory Disk I/O is low CPU Utilization is not too high (consistently in the %90s).

17. Why do we need an EMPI? Patient visits multiple separate healthcare providers Enterprise MPI Radiology Patient known as John Smythe Hospital Patient known as John Smith Laboratory Patient known as J. M. Smith Patient ID | John Smith | … Three entries merged into single record

18. Approaching Record Matching

19. Client Registry Architecture Overview of the software architecture of OpenEMPI

20. OpenEMPI Architecture Utilizing the idea of a service, interchangeable implementations of services can be plugged into the system transparently

21. Blocking Algorithms Comparison of records is quadratic in the number of records Two files of 300,000 each generate 90 billion pairs Blocking variables are used for partitioning Multiple passes are used to prevent errors Selecting blocking variables High selectivity factor Preferably uniformly distributed Wide variety of blocking algorithms available Sorted neighborhood Bigram Indexing Canopy Clustering 21

22. Field Comparison/Distance Algorithms Phonetic Encoding Algorithms Soundex: oldest and most well known algorithm Phonex: aims soundex by pre-processing names Phonix: extension of Phonex with > 100 rules NYSIIS: New York State Identification Intelligence System Metaphone/Double Metaphone Approximate String Matching Levenshtein or Edit Distance Longest Common Substring (LCS) Q-Grams Jaro/Jaro-Winkler Combinations of techniques 22

23. Matching Algorithms Variety of algorithms available, both deterministic and probabilistic Fellegi-Sunter is the most popular probabilistic algorithm 23