FinOMOP_mappings

This repository is part of a series of repositories that helps maintain the mapping of Finnish medical vocabularies to OMOP standard concepts.

flowchart LR
    A["<a href='https://athena.ohdsi.org/search-terms/start' target='_blank'>Athena</a>"]
    B["[GitHub]🔒 <a href='https://github.com/FinOMOP/OMOP_vocabularies' target='_blank'>OMOP_vocabularies</a>"]
    C["[GitHub] <a href='https://github.com/FinOMOP/FinOMOP_mappings' target='_blank'>FinOMOP_mappings</a>"]
    D["[GitHub]🔒 <a href='https://github.com/FinOMOP/FinOMOP_vocabularies' target='_blank'>FinOMOP_vocabularies</a>"]
    E[ETL]
    A --> B
    B --> C
    C --> D
    D --> E

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Other repositores are keep private as they contain proprietary data.

OMOP vocabualies are downloaded from Athena and stored in FinOMOP_vocabularies. This repository, FinOMOP_mappings, tracks the changes of mapping files in usagi-extended format for multiple vocabularies. Mapping files are transformed, appended to the OMOP vocabulary tables and stored in FinOMOP_vocabularies, for the FinOMOP members to use in their ETLs.

The repository :

• Stores mapping files in usagi-extended format (USAGI v1.4.0 format plus few additional columns) for multiple vocabularies (see).
• Stores code counts from different Finnish institutions for assessing mapping coverage.
• Automatically validates changes in the mapping files and blocks its merge if the changes are not valid.
• Automatically updates the Status Dashboard when a new release is created.
• Automatically creates a new vocabulary release in FinOMOP_vocabularies when a new release is created.
• Allows to manually update mapping files based on a new Athena release.

(this repo uses the companion R package ROMOPMappingTools)

Quick reference

For CDM users

You can see how well a vocabulary covers you data in the Status Dashboard.

For mappers

Environment setup

• Install USAGI
• Navigate to the latest releas in OMOP_vocabularies
• Download the input_omop_vocabulary.zip
• Unzip it
• Open USAGI build the index from the unzipped folder

Mapping

• 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 in FinOMOP_vocabularies
• Download the FinOMOP_vocabularies.zip
• Unzip it
• Load in your local database

For maintainers

See extended documentation in DOCUMENTATION/README.md