MedCodeMap

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

(★ 21)

PyPI Package: An easy-to-use medication/drug code mapping tool

MedCodeMap 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# MedCodeMap: Medication Code Mapping Tool

> ### We have renamed the package into "MedCodeMap".

There are many medication/drug taxonomy systems, such as RXCUI, NDC, ATC. I feel it time-consuming and very confusing to map codes between two different systems during working on this **drug recommendation project** https://github.com/ycq091044/SafeDrug. Sometimes, the code mapping resources cannot be accessible as well. To help others onboarding, here we go!

This python package provides an easy-to-use medication code mapping tool. Within the supported drug coding systems, **it provides easy functions to map from one coding system to another coding system**. Currently, we support the following drug coding systems
- ```NDC10```: the National Drug Codes system on 10-digit level
- ```NDC11```: the National Drug Codes system on 11-digit level
- ```RXCUI```: RxNorm concept unique identifier
- ```ATC4```: Anatomical Therapeutic Chemical code level-4
- ```Name```: drug string-based name, e.g., Lorazepam
- ```SMILES```: drug smiles string

For any given combination of coding systems, we will provide the mapping functions. For example
- User Input: ```NDC10```, ```RXCUI```, ```ATC4```
- Output Python Dictionary Object
    - ```NDC10_to_RXCUI```, ```NDC10_to_ATC4```, ```RXCUI_to_NDC10```, ```RXCUI_to_ATC4```, ```ATC4_to_NDC10```, ```ATC4_to_RXCUI```
---
## 1. Package Installation

```bash
# get from PyPI
$ pip install MedCodeMap
```
```bash
# local installation
$ cd ~/MedCodeMap
$ pip3 install dist/MedCodeMap-[VERSION-ID]-py3-none-any.whl
```
To look up for help, directly type "MedCodeMap" in the cmd and the help message will pop up.
```bash
$ MedCodeMap
```
## 2. Quick Usage
### Load all mappings during initialization
```python
from MedCodeMap import CodeMapping
# initialize with a list of supported coding systems
tool = CodeMapping('NDC10', 'RXCUI', 'Name', 'SMILES')
tool.load()

# we are good to go, e.g.,
tool.RXCUI_to_SMILES['312055']
tool.NDC_to_Name['76413-153-06']
...
```
### Want to add more coding systems later?
```python
# add additional coding system
tool.add_new_code("NDC11")

# we are good to go, e.g.,
tool.NDC_to_NDC11['76413-153-06']
```
- check ```test/Example.ipynb``` for examples.
- **Implementation Features --- Minimal Computation.** The tool will require minimum computation cost for generating all necessary combinations within the listed coding systems, and other mapping functions will not be generated. For example, in this demo, ```NDC11_to_RXCUI``` will not be accessible since ```NDC11``` is not listed in the user input (before). Our minimal cost computation relies on that we maintain a graph structure of the listed coding systems and use shortest path method to find the missing mapping.

## 3. Current Data Resources
The current data resources are loaded from Google Drive. We basically borrow the data from
- ```SafeDrug```: https://github.com/ycq091044/SafeDrug/tree/main/data/input
- ```DrugBank```: https://www.dropbox.com/s/angoirabxurjljh/drugbank_drugs_info.csv?dl=0
    
    ```bash
    # Google Drive Link
    https://drive.google.com/uc?id=1I2G6fsBDXDiAK95qFWwtnl3Ib2MaLeCx
    https://drive.google.com/uc?id=1d2HzsByXrPadvjaKDOEaOt78OkAZOrjC
    https://drive.google.com/uc?id=199i8mP2gMQNhwUe-2ZNmIr5fhiBbzVlK
    https://drive.google.com/uc?id=1Z11J4st1sI44jPborls9jIxzcpF-GpGt
    ```

- We are going to integrate more resources for supporting other coding systems, such as SNOMED.

MedCodeMap

MedCodeMap 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

MedCodeMap

MedCodeMap 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README