Toolkits for NCBI Pubmed
Project description
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
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