Add mappings to OMOP

[brendanreardon]

Task Description
OMOP is a very popular ontology for representing concepts related to observational research. They have an Oncology Working Group, which is likely a good place to start.

Objective and requirements
We specifically would like to provide concept mappings of therapies, cancer types, and biomarkers to OMOP.

Implementation Steps
Outline the steps or stages involved in completing this task:

1. Find the web resource version of OMOP
2. Enter relevant codings to referenced/codings for therapy, cancer types, and biomarker concepts.
3. Categorize these codings as referenced/mappings.
4. Provide these mappings within the core tables for referenced/therapies, referenced/diseases, and referenced/biomarkers.

Dependencies
N/A

Additional Context
@DavidIkechi shared several resources that have been most useful for understanding OMOP.

• https://ohdsi.github.io/Tutorial-ETL/
• https://ohdsi.github.io/TheBookOfOhdsi/CommonDataModel.html
• https://pmc.ncbi.nlm.nih.gov/articles/PMC8565035/
• https://ohdsi.github.io/CommonDataModel/faq.html

Other resources:

• Athena is a data browser for OMOP.
• Belenkaya, R. et al. 2025, Extending the OMOP Common Data Model and Standardized Vocabularies to Support Observational Cancer Research
• Ajmal, A. et al. 2025, Establishing standards: harmonising coding principles for a minimal cancer dataset in the OMOP Common Data Model
• OMOP Oncology Working Group, which includes their wiki.
• For OMOP Genomics, they also have slides on how they created it as well as a tool to help find concepts.

Priority
Low

[brendanreardon]

Koios is an R package used to identify concepts in OMOP, found out about via Marina Ainciburu.