! This is a partial copy from the private repository github.com/FinOMOP/FinOMOP_OMOP_vocabulary used for demostration and testing porpuses!

FinOMOP OMOP vocabularies

This repository helps to maintain the mapping of Finnish medical codes to OMOP standard concepts.

The repository track the changes of :

• Mapping files in usagi-extended format (USAGI v1.4.0 format plus few additional columns) for multiple vocabularies.
• Source code counts from different Finnish institutions for assessing mapping coverage.

The repository stores for each release :

• A copy of the OMOP-vocabulary tables downloaded from Athena with the vocabularies agrred by the FinOMOP group.
• A copy of USAGI v1.4.0 with prebuild indexes using the avobe tables.
• An ETL-ready instance of the OMOP-vocabulary tables with the Finnish vocabularies and selected vocabularies from Athena.
• HTML dashboard to visualize mapping status, database coverage, and quality check of files.

(this repo uses the companion R package ROMOPMappingTools)

Quick reference

For visualizing status

(at the moment)

• Download StatusReport/dashboard.html
• Open it in a web browser.

For mappers

• Navigate to the latest releas and download USAGI_with_FinnOMOP.zip
• Unzip it
• Download the wanted <vocabulary>.usagi.csv file from the correct folder in VOCABULARIES
• Open and edit in USAGI
• Save and upload back to the repository when ready

For ETL

• Navigate to the latest releas and download output_omop_vocabulary.zip
• Unzip it
• Load in your local database

For maintainers

See extended documentation in DOCUMENTATION/README.md