FAERS DRUG STANDARDIZER (AIOLI)

The FAERS drug standardizer is a tool to be used in combination with AEOLUS for a larger and more accurate mapping of the FEARS data to RxNORM CUIs and OMOP standard ingredient concept ids. It also allows for standardization to ATC rather than RxNorm. Principally it can fully replace the AEOLUS drug_mapping scripts.

Note: The master branch of this project should work, but the project as whole is still under construction. Contributions, comments and suggestions are very much welcome.

REQUIREMENTS

• Java and Maven

• Aioli builds on the AEOLUS system, so once you have used that to load the FEARS data up until the drug mapping section you can use this app to do the mapping, and then use the AEOLUS again for the final stats calculations.

• You will need the RxNORM database, in particular the RXNCONSO and RXNREL tables. The db is freely available here. The app expects the tables to be located in the same db as the aeolus data and located in a schema named rxnorm

• To map towards OMOP concept ids:

  • A database containing the RxNORM vocabulary from OHDSI. The app expects this database to be located in the same db in a schema called staging_vocabulary (this is in line with the CEM information prep step, that this app was originally built to be used for)

• To map towards ATC you need a conversion table which is available on request

HOW TO RUN

• Make sure the db is configured in accordance to your needs in the config.properties file located in scr/main/resources

• Use mvn clean package assembly:single in the present folder to build the app

• Run with java -jar target/ailoi_java-1.0-SNAPSHOT-jar-with-dependencies.jar -tv <target vocabulary> -rmin <true or false>

• Running time is approx 5 - 15 hours depending on target vocab (ATC slowest, RXNORM fastest) and the specs of your system.

OPTIONS

--target-vocab -tv The vocabulary you wish to map to valid options are ATC, RXNORM and OMOP

--retain-multi-ingredients -rmin In the original mapping section of AEOLUS the idea was to include multi-ingredient drugs in the roll up, the present implementation allows you to split the multi-ingredient drugs to single ingredient entries if you please (This option only makes a difference when targeting RXNORM or OMOP).

--skip-normalizer -sn Whether you wish to use the RxNorm API, in order to run this you need to run the RxNav-in-a-Box locally on port 4000. Otherwise, we overload the RxNav servers https://lhncbc.nlm.nih.gov/RxNav/applications/RxNav-in-a-Box.html