Searching PubMed automatically

This notebook (intended to be run on Colab: ) takes an excel file of authors and their institutions and searches PubMed for tuberculosis-related papers from those authors published during a user-specified date range. Output is:

• a semicolon-separated list of PubMed IDs, which can be pasted directly into the PubMed search box to get a page listing those papers
• a CSV file (SEATRAC_pubmed_citation_counts.csv) with citation counts and other metadata (year, title, relative citation ratio) for each paper, pulled from the NIH iCite API

More info:

• PubMed API (NCBI Entrez E-utilities) help: https://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Introduction
• More help: https://pubmed.ncbi.nlm.nih.gov/help/
• List of PubMed "tags": https://www.ncbi.nlm.nih.gov/pmc/about/userguide/