Orthopedic NLP Project

Notebook-based exploration of basic medical NLP workflows using PubMed abstracts related to total knee arthroplasty.

Contents

• 01-Basic-Text-Processing.ipynb - tokenization, normalization, lemmatization, PubMed retrieval, and simple text processing examples.
• pubmed_sample_tka_10.csv - small sample dataset of PubMed metadata and abstracts used by the notebook.
• requirements.txt - pinned Python/Jupyter/NLP dependencies.

Setup

python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
jupyter lab

The notebook uses NLTK, spaCy, Biopython, pandas, and common Python NLP tooling. PubMed requests should set a real NCBI Entrez email before running live retrieval cells.

License

MIT