If using the system, please cite:
Hannah Eyre, Patrick R Alba, Carolyn J Gibson, Elise Gatsby, Kristine E Lynch, Olga V Patterson, Scott L DuVall. Bridging information gaps in menopause status classification through natural language processing. JAMIA Open. 2024.
@article{10.1093/jamiaopen/ooae013,
author = {Eyre, Hannah and Alba, Patrick R and Gibson, Carolyn J and Gatsby, Elise and Lynch, Kristine E and Patterson, Olga V and DuVall, Scott L},
title = "{Bridging information gaps in menopause status classification through natural language processing}",
journal = {JAMIA Open},
year = {2024},
month = {02},
issn = {2574-2531},
doi = {10.1093/jamiaopen/ooae013},
url = {https://doi.org/10.1093/jamiaopen/ooae013},
}
The system is based on Leo architecture extending UIMA AS. For more info on Leo see [ http://department-of-veterans-affairs.github.io/Leo/userguide.html ] To use the system:
- Follow the instructions to install and configure UIMA AS Steps 2.1-2.9 on page [ http://department-of-veterans-affairs.github.io/Leo/userguide.html#/a2_Installation_and_Configuration_of_Leo-Example ] .
- Start UIMA AS Broker.
Open the code in IDE of your preference. We recommend using IntelliJ Community version [ https://www.jetbrains.com/idea/download ]
To run Service, right click on src/main/java/gov/va/vinci/menopause/Service and select Run Service.main()
To run Client to read from files and write to xmi, right click on src/main/java/gov/va/vinci/menopause/Client and select Run Client.main()
To run Service to read from other sources and write to a different output, readers and listeners have to be configured and then specified as Program arguments. If reading from a database, you might need to add Djava.library.path VM configuration
Client VM options:
-Djava.library.path="lib;"
-Dlog4j.configuration='config/log4j.properties'
Client Program arguments:
-clientConfigFile=config/ClientConfig.groovy
-readerConfigFile=config/readers/FileCollectionReaderConfig.groovy
-readerConfigFile=config/readers/DatabaseCollectionReaderConfig.groovy
-readerConfigFile=config/readers/SQLServerPagedDatabaseCollectionReaderConfig.groovy
-readerConfigFile=config/readers/BatchDatabaseCollectionReaderConfig.groovy
-listenerConfigFile=config/listeners/SimpleXmiListenerConfig.groovy
-listenerConfigFile=config/listeners/SimpleCsvListenerConfig.groovy
-listenerConfigFile=config/listeners/DatabaseListenerConfig.groovy
-listenerConfigFile=config/listeners/KnowtatorListenerConfig.groovy
-listenerConfigFile=config/listeners/AuCompareSummaryListenerConfig.groovy
-listenerConfigFile=config/listeners/AuCompareCsvListenerConfig.groovy