Adding PMCID to LaTeX/BibTeX/Biber bibliography

This repository contains code and working example for adding PMCID to bibliographic references compiled by LaTeX/BibTeX/Biber

Scripts and usage

• The script get_doi.pl extracts digital object identifiers (DOIs) from the bbl file. Run it as: perl get_doi.pl Your_bbl_file.bbl. It will output the DOIs in a file named DOIs_Your_bbl_file.bbl
• Take the DOIs from DOIs_Your_bbl_file.bbl and input them into https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ to extract in batch all corresponding PMCIDs. Save the output as csv file in ids.csv, which is an option of the website.
• The script add_PMCID.pl adds PMCIDs to the bbl file. Run it as: perl add_PMCID.pl ids.csv Your_bbl_file.bbl. This will output _Your_bbl_file.bbl file that should contain the PMCID added at the end of each reference that had a DOI with a corresponding PMCID.

Working example

• perl get_doi.pl Slavov_Research_Stategy.bbl
• Get PubMed IDs in batch mode from https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ and save them ids.csv
• perl add_PMCID.pl ids.csv Slavov_Research_Stategy.bbl

Customization

• This strategy requires that your bibliography outputs DOIs in the bbl file, so any modifications should preserve this feature.
• Depending on the formatting of the DOIs output in your bbl file, you may need to change the regular expressions in the perl scripts a bit.