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
Star History
1 maintainer
Metadata
1 maintainer
Release files for pypubmed 1.1.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pypubmed-1.1.8.tar.gz | 15.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pypubmed-1.1.8-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 35.7 kB
Release files / pypubmed-1.1.8.tar.gz
| Download URL | pypubmed-1.1.8.tar.gz |
|---|---|
| Size | 15.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.8
|
Release files / pypubmed-1.1.8-py3-none-any.whl
| Download URL | pypubmed-1.1.8-py3-none-any.whl |
|---|---|
| Size | 19.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
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BLAKE2b-256 checksum How to use checksums |
784eb55bb8ec667c6077d7c2b3207383fcaea53a77715ab7514106a3150ddab5
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.8
|
