KOGO_OpenAI_API_Tutorial_2025

This repository is for the Clinical Data Analysis tutorial using the OpenAI API.

It contains code and materials from the 3rd Genome Medicine Academy held in 2025 by the Korea Genome Organization (KOGO).

Presentation slides

https://docs.google.com/presentation/d/1DiOlkh-lhqpQQmcHcn5c436wPVtsygQ_/

The tutorial consists of two main sessions:

Practice Session List

[Session 1 - Clinical Note Analysis]

Description: Leveraging OpenAI models to extract clinically relevant insights from free-text medical notes. Contact: Soungmun Kim (email)

[Session 2 - Building Gene Embeddings]

Description: Leveraging OpenAI to learn low-dimensional gene representations from biomedical context.
Contact: Sungmin Kwon (email)

How to Start: Download and Open in Colab

To run the tutorial notebooks, follow these steps:

[Step 1: Download the Github Repository]

1. Click the green Code button (top right) and select Download ZIP.
2. Unzip the downloaded file on your local computer.

[Step 2: Open the Notebook in Colab]

1. Go to Google Colab
2. Click Open Colab button (top right)
3. Choose the Upload tab and upload Tutorial 1 & Tutorial 2 notebook(.ipynb) files from the unzipped folder

• Session1/Tutorial1_ExtractInfo_ClinicalNotes.ipynb
• Session2/Tutorial2_GeneEmbeddings.ipynb

4. Once uploaded, the notebook will open and is ready to run in Colab.

[Step 3: API Key Information]

The API Key required for the practice can be found at the link below.
Note: This API Key is strictly for use during the KOGO workshop sessions only.

API Key Document