zhuchcn/pubmed-bib

Convert PubMed ID (PMID) to BibTex reference

Convert PubMed ID (PMID) to BibTex Reference

This is a very simple tool that searches the given PMID(s) using PubMed's REST api, get the reference information, and convert to a BibTex format.

Installation

$ git clone https://github.com/zhuchcn/pubmed-bib.git
$ cd pubmed-bib
$ pip install -e .

Search a single PMID

A single PMID can be searched using following command.

$ pubmed-bib --id 30440093

A reference record in BibTex format will be printed in terminal.

@article{park2018evaluation,
    title={Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing},
    author={Park, Chan Hyuk and Lee, A-Reum and Lee, Yu-Ra and Eun, Chang Soo and Lee, Sang Kil and Han, Dong Soo},
    journal={Helicobacter},
    volume={},
    pages={e12547},
    year={2018}
}

Or append a reference ot an existing BibTex file

$ pubmed-bib --id 30440093 --output-file reference.bib

Batch search

A batch search can be done by providing a .txt file with a PMID in each line, and all references are ready for you.

pubmed-bib --input-file pmid.txt --output-file references.bib

pubmed-bib's Issues

Thank you!

I’ve been looking for a light-weight way to manage bibtex references from pubmed. Everything else I have found is very bloated and the code is very difficult to modify. I could easily read your code. Your style is very functionally oriented, clean and easy for me to understand. (No deeply nested classes etc.) I hope you don’t mind, but I am going to copy your function into my github repository (https://github.com/prairie-guy/sci-hub)and modify it for my own use. I will provide attribution.

Again, I just wanted you to know that I really appreciate your contribution!