Searches for articles in PubMed using an user input, and outputs an Excel table with the results. This scripts uses the python library pymed.

Script made by David Requena [02/17/2020]

The Rockefeller University. New York, USA.

Contact: [email protected] / [email protected]

This code asks the user for a query to be searched in PubMed. This can include Field Tags: https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Search_Field_Descriptions_and

Then, it retrieves the PubMed ID (PMID), publication date, the title, list of authors (separated by semicolon), journal name, DOI, keywords and abstract. And finally saves the info in a table (in MS Excel .xlsx format) in the current directory.

You need to have installed Python 3 (https://www.python.org/downloads/) and the following modules:

1. pandas -> can be installed by writting in the Terminal: pip install pandas
2. pymed -> can be installed by writting in the Terminal: pip install pymed
3. openpyxl -> can be installed by writting in the Terminal: pip install openpyxl

Just doble-click on the script to execute it. This can also be called from the Terminal. Then, the program will ask you to:

First, provide a query. Here you have two equivalent examples:

Example 1: (Fowlpox OR FPV) AND (Reticuloendotheliosis OR REV)
Example 2: (Fowlpox[All Fields] OR FPV[All Fields]) AND (Reticuloendotheliosis[All Fields] OR REV[All Fields])

Second, provide an e-mail address (optional). You can just say no.

Third, the maximum number of results desired.

I'm including an example of the output table.

This script truncates the titles and abstracts when the text has italics or special characters. For better results, check my other script search_pubmed_entrez.

I used the following links as references:

1. https://stackoverflow.com/questions/57053378/
2. https://www.kaggle.com/summerkrankin/pubmed-download-als