Tool: pubmex - a script to get a fancy paper title based on given DOI or PMID
2
gravatar for mmagnus
5.7 years ago by
mmagnus150
mmagnus150 wrote:

Hi,

If you download a pdf from the journal very often it has a cryptic name.

I guess most of us are using Mendeley etc... but if you need from time to time rename your pdf files, don't forget about pubmex :-)

Pubmex a script to get a fancy paper title based on given DOI or PMID.

If you submit DOI `10.1007/978-1-60761-863-8_2` you will get `Shepherd.Ibba.Bacterial.transfer.RNAs.FEMSMicrobiolRev.2015.pdf`.

You can use Python script to "watch" your folder for pdfs and change their names automatically.

It is very old, I think I wrote the first version 6-7 y ago :-) right now I use Mendeley, but I use the web server from time to time if I want to send a pdf to someone else.

The standalone version is here (https://github.com/m4rx9/pubmex )and the web server is here (http://pubmex.alwaysdata.net/ ).

 

 

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by mmagnus150
1

see also: https://github.com/elfar/PubmedPDF

ADD REPLYlink written 5.7 years ago by Pierre Lindenbaum133k

This really made me excited because my advisor is pretty particular about the naming the files including code, pdfs of the papers that I send him. As a result, I came up with a similar naming scheme (I guess everyone uses more or less the same scheme) that includes name of the first and last author, keywords, year and organism used. I tested your tools on few of my papers but IMHO the tool didn't give me decent file names. It keeps using the complete title of the paper that I would avoid because it is making the file name too long. Nevertheless, it is a great tool. Thanks.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Ashutosh Pandey12k

It is hard to shorten meaningfully long names. You can use `keywords`. Then the title will be replace be keywords. Please, play around with the example `keywords` from the server.

Hehe.. in my case it was the same. My boss came up with this way of naming files :-)

Since it's open source, you can take the code and change it how you like :-)

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by mmagnus150

Interesting!

Thank you for sharing ;)

ADD REPLYlink written 5.7 years ago by Deepak Tanwar4.1k
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