How do you organise scientific papers?

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I am facing the issue that my lovely tool “Papers”, which I use for managing scientific resources is only available for macOS and iOS and I am gradually switching to Linux for work; I need to be able to work on both.

The key features I definitely love are (and am used to):

  • “matching” (I can import an arbitrary PDF and Papers usually finds the reference and downloads the metadata)
  • exporting bibtex entries (this works out of the box in Papers due to the “matching” feature)
  • tagging/organising in general
  • annotating (this is optional as it can easily be done using external PDF viewers)
  • syncing (it’s convenient to be able to access everything from my phone/tablet/mac)

The downsides of my current setup are:

  • Proprietary (unable to access the data without the app)
  • Not available for Linux

I just found that there is ReadCube.com which is promoted on the Papers website but I have not figured out how to import stuff. Also I am not really happy with a web app with an online library, I prefer to have my stuff also available offline.

Long story short: how do you guys organise your papers? I am sure there are better ways…

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I use Zotero.

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Zotero! It does everything on your list, plus it’s open source. Biggest downside for me: no iOS app. (You can sync to an account and then use a web UI, but that’s not as nice as an app).

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I use Mendeley, I liked it more than Zotero. But I don’t have strong arguments why, don’t really remember anymore…

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If you are an Emacs user,

https://github.com/tmalsburg/helm-bibtex

is the perfect solution. It basically stores PDFs in filenames matching the BibTeX key of a .bib file. Transparent, open source, easy to back up, works out of the box but you can procrastinate away a whole rainy afternoon tweaking it, etc.

edit: and of course it is fully integrated into authoring papers with Emacs, and lightning fast.

For annotation, it works nicely with

https://github.com/jkitchin/org-ref

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Thanks so far! I tried Zotero but it seems it requires some lib-path adjustments on ArchLinux, I was not able to run. I then tried Mendeley which looks quite nice.

Actually the Emacs solution seems something I would definitely prefer but I am on the other side (VIM) :see_no_evil: maybe I find something for that…

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Zotero (the AUR version) works fine for me, on Manjaro.

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I used mendeley until it was acquired by Elsevier.

Now I just have one bibtex file that I open in vim with these lines in my .vimrc

autocmd FileType bib nmap <C-P> "zyy:!zathura <C-r>=substitute(substitute(@z,'.*pdf[^{]*{\([^}]*\)}.*','\1',''),'\s','\\ ','g')<CR> &<CR><CR>
autocmd FileType bib command -nargs=+ Find :vim /\c@\_[^@]*<args>\_[^@]*/g % | :cw

The first line allows me to open pdfs in zathura when I am on a line that starts with pdf and press Control-P. The second line is just a helper to find bibtex entries. The path to the pdf, tags, comments etc. I just add to the bibtex entries.

I get bibtex entries with a script that runs e.g. curl -s -LH "Accept: text/bibliography; style=bibtex" https://dx.doi.org/$DOI or queries http://api.adsabs.harvard.edu.

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Yeah, I should have looked for the AUR first :wink: I was using the binaries from their page. The AUR works fine!

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Ehm, yes I realised it after the first launch when it forced me to create an Elsevier account. No thanks :laughing:

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That’s seems like a nice workflow with on-board tools! I have to try it out…

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I played a bit with Docear, it has more a mindmapish workflow.

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If you use chrome, paperpile is awesome and integrated well with Google docs. Their development was going gangbusters for a few years, but seems to have stayed lately unfortunately. They’ve been promising an Android app and better off reader for years now. But what’s there is pretty good as is (though it costs, I have an institutional account)

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Thanks, I’ll have a look! I don’t mind to pay, as long as I am not depending on some kind of proprietary library structure which is more or less useless when I decide to switch again :wink:

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An experienced colleague of mine uses and recommends http://www.jabref.org/ I thought the install req’s where too heavy for my system but it seemed useful to organize at the level of the bibtex its self.

I use Zotero since it saves a copy of the paper its self and syncs them across devices, but I sometimes struggle with getting the bibtex out in a usable format.

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They’ve got really nice bibtex import and export - I think they’re using an open standard for PDF annotation too, but I haven’t looked into that deeply.

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Another vote for Zotero here! I also find the Zotero Better BibTex extension indispensable: https://zotplus.github.io/better-bibtex/index.html

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zotero. I’ve never had problems running it on arch.

If you use vim I wrote a zotero/bibtex integration https://github.com/rafaqz/citation.vim. It reads your zotero database so you can insert citations and open pdfs/urls directly from vim.

(it also integrates with better-bibtex citation keys)

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:+1: for zotero. I also use the “Better BibTex for Zotero” plugin.

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I use Zotero with PaperShip on IOS to view saved articles on my phone.