https://github.com/suqingdong/pypubmed
Toolkits for NCBI Pubmed
https://github.com/suqingdong/pypubmed
ncbi pubmed sci
Last synced: 6 months ago
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Toolkits for NCBI Pubmed
- Host: GitHub
- URL: https://github.com/suqingdong/pypubmed
- Owner: suqingdong
- License: mit
- Created: 2020-12-09T06:00:37.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-11-22T07:22:47.000Z (over 1 year ago)
- Last Synced: 2025-09-29T07:08:17.369Z (9 months ago)
- Topics: ncbi, pubmed, sci
- Language: Python
- Homepage: https://suqingdong.github.io/pypubmed/
- Size: 332 KB
- Stars: 29
- Watchers: 1
- Forks: 8
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# NCBI Pubmed Toolkits
## Requirements
- Python3.6+
## Installation
```bash
python3 -m pip install -U pypubmed
```
## Usage
### `search`
> search Pubmed with term
```bash
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
```bash
pypubmed advance-search --help
```
### `citations`
> generate citations for given PMID
```bash
pypubmed citations --help
```
## Todos
- [ ] HTML output
- [ ] PDF downloader
- [ ] GUI application
- [ ] Local paper manager
## Documents
> https://pypubmed.readthedocs.io/en/latest/
## Star History
[](https://star-history.com/#suqingdong/pypubmed&Date)