ScrubMed

This is a simple command line utility that makes use of BioPython to retrieve a set of abstracts, titles, PMIDs, and publication years for a given query. The results are dumped into manageble .csv files.

Keep in mind that it is possible to retrieve a very large number of records if your query is broad.

Guidelines

Read this: https://www.ncbi.nlm.nih.gov/books/NBK25497/

Limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays.

Installation

pip install ScrubMed

Usage

Usage: scrubmed.py [OPTIONS]

Options:
  -o, --output_directory PATH  Output directory to dump PubMed data
                               [required]
  -q, --query TEXT             Your query to send to PubMed. Note that your
                               query must be in double quotes. e.g.
                               ""0000/01/01"[PDAT] : "3000/12/31"[PDAT]
                               antimicrobial"  [required]
  --help                       Show this message and exit.

Example usage

This will retrieve all records from 2018 with the keywords "antimicrobial resistance". All of the resulting output will be dumped into the specified output folder.

scrubmed.py -o /home/user/scrubmed_output -q ""2018/01/01"[PDAT] : "2018/12/31"[PDAT] antimicrobial resistance"