How to Extract PubMed Citations Using Python: Using Jimmy Carter's Publications as an Example
Learn how to use Python to extract citation data from PubMed in this beginner-friendly tutorial. We’ll walk through importing a list of PMIDs (using President Jimmy Carter's publications as an example), fetching citing articles, combining author names, and saving detailed citation data to CSV and Excel. Perfect for researchers, students, and anyone curious about PubMed data extraction! 🚀
🔍 What You'll Learn:
How to use Python and BioPython to query PubMed publications
Importing PMIDs from a CSV file
Fetching citing article details like authors, titles, and journals
Exporting citation data of counts as well as individual lists of those that cited your articles
🔗 Code and Resources: Find the complete code and step-by-step guide here:
TIMELINE
0:00 - Intro
0:04 - Overview
0:54 - Getting a list of manuscripts/papers from PubMed
1:56 - Creating a new Python file
2:20 - Code overview
10:33 - Running our code
10:57 - Looking at our file with citation counts
11:23 - Looking at our file with individual citations (aka who cited Jimmy Carter articles)
11:43 - Oh no, weird encoding issues
11:53 - Fixing encoding issues in our code
12:15 - Results after fixing encoding issue
12:21 - Wrapping up
12:35 - Outro
