Build a medical knowledge graph based on Unified Language Medical System (UMLS)

Related tags

Deep Learningumlsmedical-informaticsdomain-knowledgeunified-medical-language-systemmedical-knowledge-graphumls-graph
Overview

UMLS-Graph

Build a medical knowledge graph based on Unified Language Medical System (UMLS)

Requisite

Install MySQL Server 5.6 and import UMLS data into MySQL database. Please refer to UMLS websites on how to install the UMLS database.

Installation

pip install umls-graph

Let Codes Speak

from umls_graph.dataset import make_umls_all

# MySQL database information
mysql_info = {}
mysql_info["database"] = "umls"
mysql_info["username"] = "root"
mysql_info["password"] = "{not gonna tell you}"
mysql_info["hostname"] = "localhost"

# read all UMLS table and save them to csv formatted files in a specific folder
make_umls_all(mysql_info=mysql_info,save_folder="umls_datasets")

License

The umls-graph project is provided by Donghua Chen.

NOTE: This project DOES NOT provide the UMLS data download due to the license issue. In addition, the processed data are not verified in actual clinical use. Please be response for any UMLS data use.

Owner
Donghua Chen
Dr. Chen's research interests include Medical Informatics, Natural Language Processing, Knowledge Modeling, Big Data Analysis, and Machine Learning.
Donghua Chen
GitHub Repository
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