https://github.com/dhchenx/umls-graph
Build a medical knowledge graph based on Unified Language Medical System (UMLS)
https://github.com/dhchenx/umls-graph
domain-knowledge medical-informatics medical-knowledge-graph umls umls-graph unified-medical-language-system
Last synced: 11 months ago
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Build a medical knowledge graph based on Unified Language Medical System (UMLS)
- Host: GitHub
- URL: https://github.com/dhchenx/umls-graph
- Owner: dhchenx
- License: mit
- Created: 2021-12-25T14:39:27.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-12-25T14:41:07.000Z (over 4 years ago)
- Last Synced: 2025-06-24T08:05:02.075Z (12 months ago)
- Topics: domain-knowledge, medical-informatics, medical-knowledge-graph, umls, umls-graph, unified-medical-language-system
- Language: Python
- Homepage:
- Size: 434 KB
- Stars: 21
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# 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](https://www.nlm.nih.gov/research/umls/index.html) websites on how to install the UMLS database.
## Installation
```pip
pip install umls-graph
```
## Let Codes Speak
```python
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](https://github.com/dhchenx/umls-graph).
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.