Health Ontology Mapper Installation Document (1.1)

Table of Contents

Table of Contents

Document Version History

OntoMapper Installation Instructions

Mapping Interpreter Install and Execution Instructions

Document Version History

OntoMapper Installation Instructions

• Download OntoMapper source from Recom SVN repository:

http://svn.recomdata.com/osr/OntologyMapper/trunk/IDR

• Create I2B2-OntoMapper schema per your database environment.

  http://wiki.recomdata.com/download/attachments/3866908/IDR_Schema_v1.5.gif

Execute the following scripts for Sybase IQ:

http://wiki.recomdata.com/download/attachments/3866908/I2B2DEMODATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2METADATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2WORKDATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2HIVE_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/Alter_I2B2DEMODATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/Alter_I2B2METADATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2_Metadata_Insert_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/OntoMapper_Metadata_Insert_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/Pharmacy_Cpt_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/Pharmacy_Obs_IQ.sql

Execute the following scripts for Oracle:

http://wiki.recomdata.com/download/attachments/3866908/I2B2DEMODATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2METADATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2WORKDATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2HIVE_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/Alter_I2B2DEMODATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2_Metadata_Insert_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/OntoMapper_Metadata_Insert_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/Pharmacy_Cpt_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/Pharmacy_Obs_Oracle.sql

• Configure dataSource properties per your environment in applicationContext.xml.  Both ‘dataSource’ and ‘i2b2MetadataDataSource’ needs to be modified.

WebContent\WEB-INF\applicationContext.xml

• Change the file (IRB & IACUC Approval file) upload folder in upload.properties per your environment.

src\upload.properties

• Configure the logger properties in log4j.properties.

src\log4j.properties

• Build the OntoMapper application by executing the ANT build file buildIDR.xml located under the root directory.

ant -f buildIDR.xml

• Deploy the generated IDR.war (found under root directory) onto Glassfish v2.1 server and restart the same.  ( http://dlc.sun.com/pdf/820-4334/820-4334.pdf )
• Access the OntoMapper application via the URL:

http://localhost:8080/IDR/jsp/Login.jsf

Mapping Interpreter Install and Execution Instructions

• Configure the database properties per your environment in mapper.properties found under the root directory.  User credentials for i2b2demodata and i2b2metadata schema need to be configured.

• Change the file (mapper instance xml file) upload folder property (UPLOAD_DIR) in mapper.properties per your environment.

• Configure the logger properties in log4j.properties.

src\log4j.properties

• Configure the RxNormMapper.file found under xml folder.  The ‘sourceConceptPath’ and ‘expression’ tags in RxNormMapper.file need to be configured as shown prior to execution.  The ‘expression’ tag can also be configured with a different drug name and its corresponding ‘sourceConceptPath’.  When doing so the ‘name’ tag under ‘provenance’ needs to be updated with a new name for the map.

  < inputSet >

    < sourceConceptSet >

< sourceConceptPath > \00Pharmacy\000000000P\0013118446\

</ sourceConceptPath >

    </ sourceConceptSet >

  </ inputSet >

  < scriptlet language = "RxNorm" >

< column sourceColumn = "tval_char" targetColumn = "tval_char" sourceType = "string" targetType = "string" >

  < expression > protease </ expression >

  </ column >

  </ scriptlet >

• Build the Mapping Interpreter by executing the ANT build file build.xml found under the root directory.

ant -f build.xml

• Execute the generated Mapper.jar (found under the root directory) by passing requisite parameters.  The Mapping Interpreter takes an xml file (mapper instance file) as input.

java -jar Mapper.jar file=xml\RxNormMapper.xml

• Once a mapper instance file is executed it could be re-run by supplying its id found in MAP_DIMENSION table of I2B2DEMODATA schema.

java -jar Mapper.jar id=1

• To execute the mapper for all the drugs in database use RxNormMapperBulk.xml file (found under xml folder) after configuring ‘sourceConceptPath’ as shown.

< sourceConceptPath > \00Pharmacy\ </ sourceConceptPath >