codingSystemAPIs

This repository contains Python code that allows you to retrieve and display the medical code names for ICD-10, SNOMED CT, and UMLS coding systems in various languages. This code can be used as an example for how to use the ICD, SNOMED and UMLS APIs in Python.

Table of Contents

• Motivation
• Files
• Prerequesites
• Installation
• Usage
• Contributing
• Contact
• Disclaimer

Motivation

Coding systems like ICD, SNOMED, and UMLS are excellent tools for standardizing medical nomenclature and ensuring consistency in medical documentation across various languages. However, medical records typically only store code display names in a single language, and, given that we are a centre located in Québec, Canada, display names often need to be translated between and displayed in both French and English. Therefore, this tool was created to facilitate the retrieval of medical code display names in any language using the coding systems' APIs.

Files

• code_api_requests.py: Contains functions to retrieve display names for medical codes from ICD-10, SNOMED CT, and UMLS APIs.
• Authentication.py: Handles UMLS API authentication using an API key.
• config.py: Contains configuration variables for accessing the ICD-10 and UMLS APIs.
• requirements.txt: The required python packages.
• Example.py: Demonstrates how to use the functions in code_api_requests.py.

Prerequesites

Dependencies

• Python >= 3.8
• lxml >= 5.3.0
• requests >= 2.32.2

API Access Credentials

• ICD: Register at https://icd.who.int/icdapi (see "API ACCESS") to get an access token.
• UMLS: Register at https://documentation.uts.nlm.nih.gov/rest/home.html (click "Get Your API Key") to get an API key.

Installation

1. Clone the repository:

   git clone https://github.com/kildealab/codingSystemAPIs.git
   

2. Install dependenices:

   cd codingSystemAPIs
   pip install -r requirements.txt
   

Usage

1. Set up configuration: Update the config.py file with your API credentials. Specifically, you will need to change:

   • For ICD: client_id and client_secret
   • For UMLS: umls_api_key
   • Coding system versions (optional): icd_version, umls_version, snomed_version. See config.py for more info.

2. Retrieve coding names: Import code_api_requests and use the following function calls in your code to retrieve the display name in any language from the code. An example usage is shown in Example.py.

   # Example python code
   from code_api_requests import get_icd10_display, get_snomed_display, get_umls_display
   
   get_icd_display(code="C77.0", lang='fr')) # ICD Example
   get_snomed_display(code="774007", lang='fr')) # SNOMED-CT Example
   get_umls_display(code="C0155502", lang='FRE')) # UMLS Example

3. Running the example: If you want to verify that your configuration variables have been set up properly, you can directly run Example.py. Note that if you want to use ICD-11 instead of ICD-10, you will have to uncomment the final example and change the version in config.py.

   python Example.py

Contributing

We welcome contributions! If you are interested in contributing, please fork the repository and create a pull request with your changes.

1. Fork the repository.
2. Create a new branch: git checkout -b feature-name
3. Make your changes and commit them.
4. Push your branch: git push origin feature-name
5. Create a pull request.

Lincence

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

Contact

For support or questions, please email Kayla O'Sullivan-Steben at kayla.osullivan-steben@mail.mcgill.ca.