CUIAPI Usage Guide

The CUIAPI in the UMLS Python Client provides methods to interact with Concept Unique Identifiers (CUIs) in UMLS. This guide walks you through different functionalities using the CUIAPI.

Prerequisites

Before using the API, ensure you have your API key to interact with the UMLS database. If you don’t have an API key, you can obtain one from the UMLS User Authentication page.

Setting Up

Here’s how to set up the CUIAPI class:

import os
from umls_python_client import UMLSClient

# Set the API KEY
API_KEY = "YOUR_API_KEY_HERE"

# Folder path to save files
PATH = r"C:\path\to\your\output\directory"

# Initialize the CUIAPI class with your API key
cui_api = UMLSClient(api_key=API_KEY).cuiAPI

Available Arguments for API Calls

• return_indented: Boolean to indicate if the response should be indented for readability.
• save_to_file: Boolean indicating if the result should be saved to a file.
• file_path: Path to the directory where the output files will be saved.

Note: The "rdf" format will only work with the native UMLS APIs and not with additional functions. cuiAPI currently does not support "rdf".

1. Fetch CUI Information

The get_cui_info method fetches detailed information about a specified CUI.

# Fetch CUI Information
cui_info = cui_api.get_cui_info(cui="C0011849", save_to_file=True, file_path=PATH)
print(cui_info)

2. Fetch Atoms for a CUI

This method fetches atoms related to the specified CUI with additional filtering options.

# Fetch Atoms for a CUI
cui_atoms = cui_api.get_atoms(
    cui="C0011849",
    sabs="SNOMEDCT_US",
    ttys="PT",
    language=None,
    include_obsolete=False,
    include_suppressible=False,
    page_number=1,
    page_size=25,
    save_to_file=True,
    file_path=PATH,
)
print(cui_atoms)

3. Fetch Definitions for a CUI

The get_definitions method retrieves definitions for the specified CUI.

# Fetch Definitions for a CUI
cui_definition = cui_api.get_definitions(
    cui="C0011849",
    sabs="SNOMEDCT_US",
    page_number=1,
    page_size=25,
    save_to_file=True,
    file_path=PATH,
)
print(cui_definition)

4. Fetch Relations for a CUI

This method fetches relationships for the given CUI, including relation labels and additional filters.

# Fetch Relations for a CUI
cui_relations = cui_api.get_relations(
    cui="C0011849",
    sabs="SNOMEDCT_US",
    include_relation_labels=None,
    include_additional_labels=None,
    include_obsolete=False,
    include_suppressible=False,
    page_number=1,
    page_size=25,
    save_to_file=True,
    file_path=PATH,
)
print(cui_relations)

Now you’re all set to explore and retrieve data from UMLS using the CUIAPI. Make sure to experiment with different CUIs, filters, and parameters to fully utilize the power of this API.