paperfetch can search papers from Pubmed and download papers from Sci-Hub, it also can get the reference and cited papers from a given article
Required python version
- python >= 3.6
Several python packages are requied for paperfetch
- biopython
- matplotlib
- pandas
- wordcloud
- beautifulsoup4
- requests
- retrying
- pysocks
# Clone remote repository
git clone https://github.com/liuwell/paperfetch.git
# Install required python pacakge
cd paperfetch
pip install -r requirements.txt
# Add execution path
# The path of current dir can get by shell command "pwd"
echo "export PATH=$PATH:current_dir/paperfetch" >> ~/.bashrc
source ~/.bashrc
paperfetch have two modules to fetch paper's information.
paperfetch.py -h
usage: paperfetch.py [-h] -t string [-p string] [-cutoff float]
[-RetMax integer] [-wordcloud] [-download]
A tool for fetch academic papers from Pubmed
optional arguments:
-h, --help show this help message and exit
-t string, --term string
the search term, Entrez text query
-p string, --prefix string
the prefix of output (default: Pubmed)
-cutoff float Set the cut off of paper's journal impact factor
(default: 0)
-RetMax integer return max number of papers (default: 1000)
-wordcloud perform worldcloud plot for paper's abstract
-download download pdf files
# generate a txt file with search result
paperfetch.py -t "small RNA[title]" -p smallRNApaperfetch.py -t "small RNA[title]" -p smallRNA -cutoff 3paperfetch.py -t "small RNA[title]" -p smallRNA -cutoff 3 -downloadpaperfetch.py -t "small RNA[title]" -p smallRNA -cutoff 3 -wordcloudpaperlink.py -h
usage: paperlink.py [-h] -pmid integer [-link {cited,refs}] [-prefix string]
[-cutoff float] [-wordcloud] [-download]
Searching for the cited papers or reference papers in Pubmed
optional arguments:
-h, --help show this help message and exit
-pmid integer Pubmed id of a specific paper
-link {cited,refs} the linked database (default: cited)
-prefix string the prefix of output (default: Pubmed)
-cutoff float Set the cut off of paper's journal impact factor
(default: 0)
-wordcloud perform worldcloud plot for paper's abstract
-download download pdf files
paperlink.py -pmid 29570994 -link citedWe found 552 cited papers in the PubMed database
The cut off of IF is 0, remained papers: 552
ID PMID PublishDate Journal IF Title Abstract
0 1 33632232 2021 Feb J Nanobiotechnology 6.518 A paclitaxel and microRNA-124 coloaded stepped... BACKGROUND: Triple negative breast cancer (TNB...
1 2 33628737 2021 Feb Front Oncol 4.848 The Paradoxical Behavior of microRNA-211 in Me... Cancer initiation, progression, and metastasis...
2 3 33614707 2021 Jan Front Mol Biosci 4.188 Intercellular Communication by Vascular Endoth... Respiratory diseases and their comorbidities, ...
3 4 33613718 2021 Mar Oncol Lett 2.311 Association between microRNA-527 and glypican-... The present study aimed to identify the specif...
4 5 33603718 2021 Jan Front Microbiol 4.235 Probiotics and MicroRNA: Their Roles in the Ho... Probiotics are widely accepted to be beneficia...
.. ... ... ... ... ... ... ...
547 548 29795674 2018 May PLoS One 2.740 Human microRNAs preferentially target genes wi... MicroRNAs (miRNAs) are short, endogenous RNAs ...
548 549 29725042 2018 May Sci Rep 3.998 Reduced Autophagy by a microRNA-mediated Signa... Autophagy plays a key role in the pathogenesis...
549 550 29702599 2018 Apr Int J Mol Sci 4.556 Noncoding RNA:RNA Regulatory Networks in Cancer. Noncoding RNAs (ncRNAs) constitute the majorit...
550 551 29692333 2018 Oct Trends Endocrinol Metab 11.641 miR-33: A Metabolic Conundrum. The miR-33 microRNAs (miRNAs) are crucial regu...
551 552 29601548 2018 Mar Biomedicines 4.717 Roles of NF-kappaB Signaling in the Regulation... The NF-kappaB family of transcription factors ...
[552 rows x 7 columns]
paperlink.py -pmid 29570994 -link refsWe found 402 refs papers in the PubMed database
The cut off of IF is 0, remained papers: 402
ID PMID PublishDate Journal IF Title Abstract
0 1 29887379 2018 Jul Cell 38.637 A Network of Noncoding Regulatory RNAs Acts in... Noncoding RNAs (ncRNAs) play increasingly appr...
1 2 29483647 2018 Mar Nat Struct Mol Biol 11.980 MicroRNA degradation by a conserved target RNA... microRNAs (miRNAs) repress target transcripts ...
2 3 29351846 2018 Jan Mol Cell 15.584 Dual Strategies for Argonaute2-Mediated Biogen... While Slicer activity of Argonaute is central ...
3 4 29298863 2018 May FASEB J 4.966 Dual regulation of HMGB1 by combined JNK1/2-AT... In the context of diabetes, obesity, and metab...
4 5 29288704 2018 Mar Exp Hematol 2.820 The mirn23a and mirn23b microrna clusters are ... Mice deficient for microRNA (miRNA) cluster mi...
.. ... ... ... ... ... ... ...
397 398 10706289 2000 Feb Nature 42.778 The 21-nucleotide let-7 RNA regulates developm... The C. elegans heterochronic gene pathway cons...
398 399 10642801 1999 Dec Dev Biol 2.895 The lin-4 regulatory RNA controls developmenta... lin-4 encodes a small RNA that is complementar...
399 400 9054503 1997 Mar Cell 38.637 The cold shock domain protein LIN-28 controls ... Mutations in the heterochronic gene lin-28 of ...
400 401 8252622 1993 Dec Cell 38.637 Posttranscriptional regulation of the heteroch... During C. elegans development, the temporal pa...
401 402 8252621 1993 Dec Cell 38.637 The C. elegans heterochronic gene lin-4 encode... lin-4 is essential for the normal temporal con...
[402 rows x 7 columns]
Thanks for Biopython's Entrez module and Sci-Hub API.