pubid2bib 0.0.1

Description:

pubid2bib 0.0.1

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