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callahantiff / OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

http://tiffanycallahan.com/OMOP2OBO_Dashboard

MIT License

84 stars 12 forks source link

Closed callahantiff closed 4 years ago

callahantiff commented 4 years ago

Task: Add Jupyter Notebooks for the following:

[x] Running the mapping pipeline -- take existing content from main.py and organize it in a similar fashion as done for PheKnowLator (we've had good feedback that this approach is user friendly)
[x] Performing coverage studies using Concept Prevalence data
[x] Aligning outside OMOP concepts to the current main mapping file and outputting useful information for next steps

callahantiff commented 4 years ago

[x] Running the mapping pipeline -- take existing content from main.py and organize it in a similar fashion as done for PheKnowLator (we've had good feedback that this approach is user friendly)

Completed notebook: omop2obo_notebook

callahantiff commented 4 years ago

add Zenodo links for preprocessed ontology data to notebook for those who want to replicate our process

callahantiff commented 4 years ago

Done!