bib2item3

DESCRIPTION

Script to reformat Bibtex reference library into bibitems for specific scientific journals. Supports only Protein Science at this time.

BACKGROUND

The ScholarOne Manuscript vendor used by Protein Science does not accept Bibtex library files. Per the authors' instructions, you are stuck with using a bibliography environment and bibitems. The bibitems are tedious and error-prone to assemble by hand.

The tex Stackexchange user Ixy published online a python2 script that I repurposed for Protein Science and python3. It is not all-inclusive. Many edge cases remain unaddressed. You will still have to check all references manually.

There are other solutions to this problem. You should be able to generate a *.bbl file from your lib file by running LaTeX, BibTeX, latex, and latex on your bib file. The *.bbl file contains the bibitems. I recommend using this approach whenever possible. It is superior to the solution provided by my script. However, I had no luck with this approach at 1 AM on the night of manuscript submission.

There is also a Matlab solution. I did not have access to Matlab at the time that I found this solution. Perhaps this solution can be run with an octave.

Source of original script:

Author of inspiring code : Ixy, a secretive tex StackExchange user.

USAGE

bib2item3.py refs.bib

Notes:

• The bib file should have only the citations that you want to include in your manuscript.
• The names of the journals should have the proper abbreviations.
• The citations in the bib file should be in alphabetical order because this script does not sort them.
• You should be able to copy the output into a bibliography environment in your LaTeX file.

To Be Done

• run flake8 and edit
• run pylint and edit
• develop test functions
• improve error handling

Update history

Version	Changes	Date
Version 0.2	Added badges and update table. Corrected more typos. Merged pull request by Melodie Chen-Glasser. Her improvements are listed in the doc string in the script.	2024 May 7

Funding

• NIH: R01 CA242845, R01 AI088011
• NIH: P30 CA225520 (PI: R. Mannel); P20GM103640 and P30GM145423 (PI: A. West)