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OmopVocabMapper

DOI

OmopVocabMapper is a Julia package for mapping various medical vocabularies to the OMOP standard vocabulary. It provides functionalities to convert terminology codes from different sources, starting with ICD (International Classification of Diseases) to the corresponding OMOP concept IDs, with the ability to indicate ICD codes that map to multiple OMOP concept IDs.

Features

  • Mapping ICD codes to OMOP concept IDs: The library currently supports the mapping of ICD9CM and ICD10CM codes to their respective OMOP concept IDs.
  • Reusability: We are actively working on expanding the functionality to support mapping of additional vocabularies like RXNORM, CPT, NDC, and more, making the library versatile and adaptable to different terminologies.

Usage

Preparing the Data

Ensure you have the following CSV files in your working directory:

  • icd_codes.csv
  • CONCEPT.csv
  • CONCEPT_RELATIONSHIP.csv

icd_codes.csv File Format

When using the map_icd_to_omop function, you need to provide a CSV file that contains ICD codes and their corresponding system types. The CSV file can have any name, but make sure to specify the correct file path and name when using the function.

Mandatory Columns:

  1. ICD: This column should contain the ICD codes. Important: Make sure that codes like 428.0 or those with leading zeros (e.g., 012.5) retain their format. This often happens when editing CSV files in spreadsheet software (like Excel) that might automatically remove trailing zeros or convert codes to numbers. Be cautious when creating the CSV file to ensure the ICD codes are preserved correctly.

  2. system: This column should specify the ICD code system used for each code. The values should be either ICD9CM or ICD10CM.

Example:

Your CSV file should look like the following:

ICD system
428 ICD9CM
428.0 ICD9CM
I50.9 ICD10CM
012.5 ICD9CM
J44.1 ICD10CM

Important Notes:

  • Make sure the ICD column preserves both numeric and alphanumeric codes exactly as they are, without removing decimal points or leading/trailing zeros.
  • The system column specifies the version of ICD codes, either ICD9CM or ICD10CM.
  • Ensure your CSV file is properly saved, and provide the correct path and file name when calling the map_icd_to_omop function.
  • It can also have other columns like name.

Downloading the vocabulary files from Athena

Running the Mapping

  1. Include the module and use it in your script or Julia REPL:

    using Pkg
Pkg.add("OMOPVocabMapper")
using OMOPVocabMapper

  2. Call the map_icd_to_omop function:

    map_icd_to_omop(
    "path/to/icd_codes.csv",
    "path/to/concept.csv",
    "path/to/concept_relationship.csv",
    "path/to/output/omopmappedcodes.csv"
)

License

This project is licensed under the MIT License - see the LICENSE file for details.

Reference

Thakkallapally M, Bradenday J, Aluthge D, Sarkar IN, Crowley KM, Chen E. OMOPVocabMapper: A Tool for Mapping ICD Codes to OMOP Concepts. AMIA 2024 Annual Symposium. [Poster Abstract] - Accepted