Eureka! Clinical Ontology Installation Files

Georgia Clinical and Translational Science Alliance (Georgia CTSA), Emory University, Atlanta, GA

What does it do?

It specifies Eureka! Clinical's extensions to the i2b2 metadata schema. It specifies an electronic health record data model and set of terminologies. It also contains liquibase XML changelog files for creating i2b2 metadata schema tables with those extensions (in src/main/resources/dbmigration).

Latest release:

Version 2.0.2

Update the parent pom.

Version 2.0.1

Fix missing close Oktousevalues tag in the C_METADATAXML for LOINC 731-0. It was causing a parsing exception in aiw-i2b2-etl.

Version 2.0

Changes the metadata schema to support improved performance of SQL statements to retrieve concepts.

Version 1.2

Initial version, with various bug fixes.

Build requirements

• Oracle Java JDK 8
• Maven 3.2.5 or greater

Runtime requirements

• Oracle Java JRE 8
• Liquibase 3.3 or greater
• One of the following relational databases:
  • Oracle 11g or greater
  • PostgreSQL 9.1 or greater
  • H2 1.4.193 or greater (for testing)

Building it

The project uses the maven build tool. Typically, you build it by invoking mvn clean install at the command line. For simple file changes, not additions or deletions, you can usually use mvn install. See https://github.com/eurekaclinical/dev-wiki/wiki/Building-Eureka!-Clinical-projects for more details.

Creating an i2b2 metadata schema with Eureka! Clinical extensions

1. Create a schema and a user account for accessing that schema.
2. Get a JDBC driver for your database and put it the liquibase lib directory.
3. Create the TABLE_ACCESS table by execute the following from the liquibase installation:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/create-table-access-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

4. Next, add the Eureka! Clinical extra tables to the schema:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/i2b2-meta-schema-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

5. Install the demographics concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_DEMOG-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

6. Install the ICD-10-CM concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_ICD10CM-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

7. Install the ICD-10-PCS concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_ICD10PCS-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

8. Install the ICD-9-CM concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_ICD9D-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

9. Install the ICD-9 procedure concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_ICD9P-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

10. Install the medication order concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_MED_ORDERS-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

11. Install the lab test concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_LABS-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

12. Install the vital signs concepts:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-EK_VITALS-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

Adding breakdown paths to the data schema

Assuming you already have an i2b2 data schema, run the following:

./liquibase \
      --driver=JDBC_DRIVER_CLASS_NAME \
      --classpath=/path/to/jdbcdriver.jar:/path/to/eurekaclinical-ontology-<version>.jar \
      --changeLogFile=dbmigration/eureka-ontology-QT_BREAKDOWN_PATH-changelog.xml \
      --url="JDBC_CONNECTION_URL" \
      --username=DB_USER \
      --password=DB_PASS \
      update

Maven dependency

<dependency>
    <groupId>org.eurekaclinical</groupId>
    <artifactId>eurekaclinical-ontology</artifactId>
    <version>version</version>
</dependency>

Data model

The electronic health record data model is described at https://github.com/eurekaclinical/eurekaclinical-ontology/blob/master/spec/Data%20model.md.

Terminologies provided

Name	Version	Source
ICD9-CM diagnosis codes		Analytic Information Warehouse project, circa 2010
ICD9 procedure codes		Analytic Information Warehouse project, circa 2010
ICD10-CM diagnosis codes	2015	UMLS 2015AA release, obtained from the NCBO BioPortal Ontology to i2b2 File Mappings page
ICD10-PCS procedure codes	2015	UMLS 2015AA release, obtained from the NCBO BioPortal Ontology to i2b2 File Mappings page
NCATS ACT lab test hierarchy (LOINC codes)	1.3	https://ncatswiki.dbmi.pitt.edu/acts/wiki/DataHarmonization
NCATS ACT NDF-RT/RxNorm hierarchy	1.3	https://ncatswiki.dbmi.pitt.edu/acts/wiki/DataHarmonization
Demographics	1.0	Locally developed, based on the i2b2 1.5 demo data ontology
Vital signs		Locally developed

Extensions to the i2b2 metadata schema

See Metadata extensions spec.md.

Running liquibase with the changelog files

There are two ways to run liquibase on Eureka! Clinical project, both described in the liquibase documentation:

• from the command line
• using maven.

Getting help

Feel free to contact us at help@eurekaclinical.org.