Linux如何在与COVID-19对抗的文献搜索中做出贡献?

COVID-19的文献每天都在增加。

使用术语COVID-19进行的PubMed搜索可产生约10,750个结果(截至IST 5月11日-19:20)。

正在考虑利用Linux的强大功能以更快的方式搜索COVID-19文献​​的有效方法,以帮助科学家。

PubMed offers a connection to the UNIX terminal through the ncbi-entrez-direct package distributed through the apt repository. Documentation can be found here. Installation is as follows.

sudo apt install ncbi-entrez-direct

Then I was thinking of searching COVID-19 articles for new targets and then looking for the word Spike inside that through the grep function of UNIX and then piping it to a file. Spike is a coronavirus receptor which is one of the main targets for COVID-19 (Reference). I also wanted to print 2 lines above and 2 lines below for understanding the context.

esearch -db pubmed -query "COVID-19 AND target" |   efetch -format abstract | egrep -i '^(Spike|"spike protein"|spike)' -A 2 -B 2 >> "Store1.txt"

这产生了以下结果

proprotein convertase furin, reducing its dependence on target cell proteases for
entry. The high hACE2 binding affinity of the RBD, furin preactivation of the
spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain
efficient cell entry while evading immune surveillance. These features may
contribute to the wide spread of the virus. Successful intervention strategies
--

The pandemic coronavirus SARS-CoV-2 threatens public health worldwide. The viral 
spike protein mediates SARS-CoV-2 entry into host cells and harbors a S1/S2
cleavage site containing multiple arginine residues (multibasic) not found in
closely related animal coronaviruses. However, the role of this multibasic
--
immunity responses (decoy cellular vaccination) in the prevention of COVID-19
disease is currently being explored. Our approach entails utilizing SARS-CoV-2
Spike antigen-expressing, non-replicating cells as carriers and presenters of
immunogenic antigens, so called "I-cells". By using irradiated cells as
presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these 
--
mechanism across the CoV family make it a valuable target to elucidate and
develop pan-CoV therapeutics. In this article, we review the role of the CoV
spike protein in mediating fusion of the viral and host cell membranes,
summarizing the results of research on SARS-CoV, MERS-CoV, and recent
peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be
--
The outbreak of a novel coronavirus (2019-nCoV) represents a pandemic threat that
has been declared a public health emergency of international concern. The CoV
spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and 
diagnostics. To facilitate medical countermeasure development, we determined a
3.5-angstrom-resolution cryo-electron microscopy structure of the 2019-nCoV S

虽然我上面引用的示例可能是基本的。我相信,如果我们要在这个论坛上提出更多建议,国际科学家可能会使用它来提高其对抗COVID-19(共同的敌人)的效率。

使用终端搜索的优势:

  • Power of awk and sed can be brought in
  • Faster than even PubMed search
  • To the point results can be obtained
  • Ability to utilize shell scripting (#!/bin/sh) and crontab for routine checking for any new results without the manual requirement to have a look into PubMed.
  • pdfgrep can be brought into action to read many pdfs at a time and many more. For eg pdfgrep "Spike" * can be used for searching for the "spike" (protein) word in all the PDF's present in the directory.

    Let's show our power of Ubuntu!!!

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