pubmed_jekyll

Uses biopython package in Python (3.x+) to search for all papers by a given author to populate a .yml file for Jekyll static pages.

Pubmed search for citations from author in Pubmed using Biopython package for populating a .yml file for Jekyll page templates. This will create a ./_data/ folder as is common in Jekyll sites.

Retreives the following info:

• Authors: Last and Forename of first author. If fewer than 4 authors, list all.
• Article Information: Title.
• Journal Information: Journal abbreviation, Volume, Issue, Pagination (if present) and year.
• DOI Link if it exists.
• Abstract Text: Only in --verbose mode, and will only be printed (not in yml file)

Saves information to _data/papers.yml unless --do_not_populate (only prints results)

Usage:

1. Straight from Python.
   >>> python pubmed_author_papers.py [email protected] 'LastName AB' --max 10 -v -d

2. Using the bash file (please change the search.sh file information to suit your needs).
   >>> bash search.sh

Arguments:
email str - Valid email for use of NCBI database search.
author str - Author information formatted "LastName INITIALS".
--max int - Maximum number of articles to search.
-v --verbose - If specified, print out article information.
-d --do_not_populate - If specified, will not populate the papers.yml