How to download PubMed baseline data using rsync

PubMed raw data is hosted on the NCBI servers which provide convenient access using rsync.

Download PubMed baseline data using a rsync command like

rsync -Pav ftp.ncbi.nlm.nih.gov::pubmed/baseline/\*.xml.gz Pubmed/

This example command will download all baseline data files as .xml.gz to the PubMed folder

You can explore the PMC directory structure by accessing the NCBI FTP server using your browser.

If this post helped you, please consider buying me a coffee or donating via PayPal to support research & publishing of new posts on TechOverflow