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.
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.
pip install ScrubMed
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.
This will retrieve all records from 2018 with the keywords
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"