pubmed-miner

Python code for make table data of pubmed article analysis. What i do is just connect two tool.

Tools that I use.

Biopython

 @article{cock2009biopython,
  title={Biopython: freely available Python tools for computational molecular biology and bioinformatics},
  author={Cock, Peter JA and Antao, Tiago and Chang, Jeffrey T and Chapman, Brad A and Cox, Cymon J and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and others},
  journal={Bioinformatics},
  volume={25},
  number={11},
  pages={1422--1423},
  year={2009},
  publisher={Oxford University Press}
} 

BERN2

@article{sung2022bern2,
    title={BERN2: an advanced neural biomedical namedentity recognition and normalization tool}, 
    author={Sung, Mujeen and Jeong, Minbyul and Choi, Yonghwa and Kim, Donghyeon and Lee, Jinhyuk and Kang, Jaewoo},
    year={2022},
    eprint={2201.02080},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}

PDM for package management

more detail at https://pdm.fming.dev/

Mode of action

python pubmed_miner.py

1. Ask user input for Pubmed query.
2. Biopython entrez module return bunch of article's pmid.
3. After that BERN2 used biological text analysis and return json file.
4. pandas used for trim the data and save csv file.