NCBI Pubmed Toolkits

Requirements

• Python3.6+

Installation

python3 -m pip install -U pypubmed

Usage

search

search Pubmed with term

pypubmed search --help

########## search pubmed ##########
pypubmed search ngs -l 5 -o ngs.xlsx
pypubmed search 'NGS[Title] AND Disease[Title/Abstract]' -o ngs_disease.xlsx
pypubmed search 1,2,3,4
pypubmed search pmid_list.txt

########## search pmc ##########
# parse pmc xml, maybe network error
pypubmed -d pmc search PMC10914497,PMC11572642
pypubmed -d pmc search pmcid_list.txt
pypubmed -d pmc search '(single cell) OR (scrna) OR (scRNA seq)'

# convert pmcid to pmid, then parse pubmed xml, some pmcid may not have pmid
pypubmed -d pmc search '(single cell) OR (scrna) OR (scRNA seq)' --convert-pmc

# do not translate
pypubmed search -l 5 ngs

# translate with a local proxies
pypubmed -p http://127.0.0.1:1081 search ngs -l 5

advance-search

advance search builder

pypubmed advance-search --help

citations

generate citations for given PMID

pypubmed citations --help

Todos

• HTML output
• PDF downloader
• GUI application
• Local paper manager

Documents

https://pypubmed.readthedocs.io/en/latest/

Star History