AEOLUS

This the EMC fork of the AEOLUS system which allows you tosStandardize the FDA LAERS database and FAERS database drugs, indications, reactions and outcomes to OMOP Common Data Model V5 concepts and generate the unique case report counts and safety signal statistics

Original detailed documentation is in the documentation folder.

Shortened updated docs are here:

Requirements

• Linux or Mac. This process was developed for Ubuntu 14.04 but has since also sucessfully run on MacOS Big Sur and Ubuntu 18.04
• PostgreSQL version 9.3 or greater

How To Run

Load Reference Data

• FDA Orange book
  • Load NDA reference data file into a PostgreSQL table called “nda” to look-up ingredients by NDA number Download the data file from the FDA Orange book website. Run load_nda_table.sql to load the data file:
• Country codes
  • Run load_country_code_table.sql to load the reference table.
• EU drug name/active ingredient table
  • Download the most recent EU drug name/active ingredient table Load the EU drug name/active ingredient reference table by running the script: load_eu_drug_name_active_ingredient.sql
• OHDSI CDMV5 Vocabulary
  • Load the latest available OHDSI CDMV5 Vocabulary tables into a separate PostgreSQL schema (e.g. cdmv5). The vocabulary data files and the PostgreSQL table load scripts are available from the OHDSI Athena website On the Athena website vocabulary download page select the MedDRA, RxNorm, SNOMED (and if you will map to ATC also download ATC) vocabulary ( review the EULA link for MedDRA).
• MedDRA / Snomed mapping
  • Create the meddra / snomed mapping table by running the script create_meddra_snomed_mapping_table.sql

Load Source Data

From the load_data_files_from_website_folder:

• Run dowload_all_and_create_files.sh
• Run all the load_current ... .sql files
• Run all the load_legacy ... .sql files
• Run delete_deleted_records.sql

Deduplicate and Impute

From the handle_duplicate_cases folder:

• Run derive_unique_all_case.sql

Mapping

Use this app https://github.com/mi-erasmusmc/aioli or refer to original docs in the documentation folder

Standardization and statistic generation

• Run standardize.sh

Contributions

Principally contributions are very welcome. If you come across issues have suggestions for improvements send a message, raise an issue or create a pr