nlpie-research / umls-to-snomed-icd10-mapper

UMLS to SNOMED CT and ICD-10 mapping tool: A Python script for generating JSON files containing mappings between UMLS CUIs and SNOMED CT or ICD-10 codes using the UMLS Metathesaurus. Supports exact match, broad relations, and parent-child hierarchy mapping methods.

UMLS to SNOMED CT and ICD-10 Mapper

This Python script maps UMLS codes to SNOMED CT and ICD-10 codes using the UMLS Metathesaurus. The program generates JSON files containing the mappings based on one of the following methods: exact match (EXACT), broad relations (RO), or parent-child hierarchy relations (PAR_CHD). The output will consist of two JSON files for each method, one for SNOMED CT mappings and another for ICD-10 mappings.

Prerequisites

To run this program, you need to request access to the UMLS Metathesaurus from the National Library of Medicine. Once you have access, download the MRCONSO.RRF and MRREL.RRF files and place them in a directory on your local machine. For EXACT matches you would only need MRCONSO.RRF.

Configuration

In the umls_mapping_tool.py file, set the UMLS_KB_PATH variable to the path of the directory where you have placed the MRCONSO.RRF and MRREL.RRF files:

UMLS_KB_PATH = "/path/to/your/directory/"

Usage

To run the script, execute the umls_mapping_tool.py file in your Python environment:

python umls_mapping_tool.py

By default, the script will use the EXACT mapping method. To change the mapping method, modify the method variable in the script:

method = "RO"  # Choose method: "RO", "PAR_CHD", or "EXACT"

The script will generate two JSON files for the specified method. For example, if you choose the EXACT method, the output files will be named cui_to_snomed_EXACT.json and cui_to_icd10_EXACT.json.