pubid2bib

pubid2bib (Publication Identifier to BibTeX) is a command line tool to fetch bibliographic entries for given publication identifiers using online services offered by PubMed, DOI and Google.

Usage:

pubid2bib publicationId1 publicationId2 ... publicationIdN

Where publicationIds are well formed PMIDs or DOIs for scientific papers or ISBNs for books.

Example:

pubid2bib 31726262 10.1021/acs.jced.5b00684 0735619670

Will create three BibTeX files in the current path, named:

• "Removal of dental alloys and titanium attenuates trace metals and biological effects on liver and kidney.bib"
• "Thermodynamic Properties of R-227ea, R-365mfc, R-115, and R-13I1.bib"
• "Code Complete.bib"

The filenames will be the publication's titles and the bibliographic entries will conform to Bibtex @article and @book formats.

Install

pubid2bib is a standalone Python script. You need Python 3 installed and you need to be able to execute Python scripts on your platform.

Inspiration

The fantastic web service TexMed allows to search scientific articles in PubMed and create BibTex bibliographic entries for them. This was the inspiration for pubid2bib.

In one sense, pubid2bib is more limited, it needs you to find the publication identifiers first, to create the BibTex entries. But, it is more general in another sense, because you can use DOIs for published scientific articles that are not found in PubMed and also ISBNs for books. Furthermore, pubid2bib can be called from scripts.

Scripting

From bash

Asumming you have a file called publications.txt with publication identifiers in each line, e.g.:

38942015
38917788
38935715

You can have a bash script that calls pubid2bib for each identifier:

#!/bin/bash

input="publications.txt"

while read -r pmid
do
    echo "${pmid}"
    pubid2bib "${pmid}"
done < "$input"

From Python

You can use the function dispatch for each identifier

#!/usr/bin/env python


if __name__ == '__main__':
    from pubid2bib import dispatch
    with open('publications.txt', 'r') as file_object:
        try:
            paperIds = file_object.readlines()
            for pid in paperIds:
                print(pid[:-1])
                dispatch(pid[:-1])
        except (IOError, OSError):
            print('Error reading file')

Abbreviations

PMID: PubMed identifier

DOI: Digital Object Identifier

ISBN: International Standard Book Number