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This question is borderline TeX related but I think it may still be relevant.

What is the best citation manager to use in conjunction with LaTeX? The cutting edge in citation management software at the moment seems to be Mendeley and Papers.

Apart from the fact that the latter is comparatively expensive, both softwares seem to offer next to no BibTeX support. Sure, they allow exporting (or even maintaining) .bib files mirroring the library but those files aren’t really usable in common scenarios (e.g. when you need to manipulate the typography, when specifying the sort key by inserting TeX commands in the authors list, or when you want to customise the citation key).

On the other hand, these citation managers have a very handy feature: when you drag a PDF onto them, all metadata (title, author …) of the article is automatically imported from online databases and doesn’t need to be added manually or by explicitly downloading an exportable citation from the journal website.

So far, my go-to choice has been BibDesk which is a solid little software. But it seems that BibDesk doesn’t support the Mendeley-style automatic import of article metadata for PDFs. Instead, I have to enter all this information manually. This becomes old quickly.

Turns out to be wrong! – See answers below.

So, Is there a citation manager which plays nicely with BibTeX and has automatic metadata import?

(Incidentally, I don’t want to complain about BibDesk, it’s otherwise an excellent software and it being Open Source the correct answer would of course be “well, submit a patch / pull request for this feature”. But perhaps somebody has already done the work?)

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To make this a question useful to all users, it would be nice if solutions could be provided for all major operating systems: Mac, Windoze, and Unix. –  Marc van Dongen Jan 26 '12 at 14:19
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possible duplicate of LaTeX and bibliography management tools –  percusse Jan 26 '12 at 14:30
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@percusse To the extent that the linked question is explicitly about non-Mac solutions, I don't think this can be a duplicate. –  Alan Munn Jan 26 '12 at 14:35
    
@AlanMunn Indeed, as I said in the chat, it's a quick reference for the voters to decide. My opinion was based on the fact that JabRef is Java based hence is an answer. But that might not count as a duplicate having the same answer. –  percusse Jan 26 '12 at 19:19
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6 Answers

up vote 11 down vote accepted

Give BibDesk another chance.

It's highly integrated with Google Scholar and other search engines. In case you need to keep the .pdf-files in your local library, just drag them onto the publication and BibDesk automatically files them for you.

Apart from the full-text-search right from BibDesk I really like the integration with the pdf-reader Skim. All the highlighted text and annotations can be viewed directly from within BibDesk. Plus, you can search through them.

You can even view your Skim-notes direclty in BibDesk's preview-pane, if you use this BibDesk-template: http://ug.bu.edu/blog/lingtech/2009/03/22/even-better-bibdesk-preview-pane

TL;DR: I heart BibDesk.

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Indeed, I’ve noticed. BibDesk is teh hotness … ♥ I was just too stupid to notice that you could drag PDF files onto it. –  Konrad Rudolph Jan 26 '12 at 15:00
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JabRef also supports metadata extraction and works on Linux, Mac, and Windows (and maybe others).

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yes, JabRef does not have the polished and OS X-native interface like BibDesk, however its big advantage is, that it is platform independent which makes it very useful for people working on several different OS's. I always got error message when trying to open a bibtex file created by JabRef with BibDesk –  Martin Jan 26 '12 at 14:38
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Not having a mac like interface is a good thing for some people. Just saying. –  Canageek Jan 26 '12 at 15:30
    
@Canageek On a Mac? Not really. If you don’t like Mac-like interfaces (legitimate) then the only real solution is not to use a Mac. –  Konrad Rudolph Jan 26 '12 at 16:25
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@KonradRudolph Sorry, I'm looking and I don't see where it says that this question is mac specific, am I missing that? I'm sick of people using mac interfaces in windows (iTunes, Safari,various open source software that wants to look shiny) –  Canageek Jan 26 '12 at 18:15
    
@KonradRudolph The question doesn't say MAc, but I am pretty sure BibDesk and Papers are both Mac only. –  StrongBad Jan 26 '12 at 19:11
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There is a wikipedia article that seems to address at least part of your question: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software

JabRef and KBibTex seem particularly interesting. Both have had a recent stable release and support BibTeX.

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I need to answer this question myself because I am stupid.

BibDesk supports all the features I wanted. It simply never occurred to me to try this out, I’d simply always manually imported references instead of just trying to drag a PDF onto it. I feel like deleting the question but perhaps somebody else finds this useful after all.

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Given that your question does appear to make BiBDesk look bad, (which it turns out it's not) and could create a false impression I'd suggest either deleting it or editing it heavily to be more constructive. –  Alan Munn Jan 26 '12 at 14:33
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@Konrad Rudolph +1 for the self-awareness and for the information. :-) You should edit the question accordingly to avoid discrediting BibDesk . –  Martin Jan 26 '12 at 14:40
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@Martin (and Alan) What about the edit I’ve made? Is the crossing out good enough? I don’t really want to remove the original question to not give a false impression. But maybe there is a nice way of reformulating it without losing the information that I’d simply overlooked this feature. –  Konrad Rudolph Jan 26 '12 at 14:50
    
@KonradRudolph: well it's better, but IMHO you should make clear what makes a "modern" citation manager from your point of view. (Like displaying and annotating pdf or adding notes to the cited sources, even with references to pages or included images, etc...) –  Martin Jan 26 '12 at 15:08
    
I agree with @Martin It would be better to list some of the features you wanted and ask if BiBDesk implements them. Then you can say Yes. :-) –  Alan Munn Jan 26 '12 at 15:11
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Good read everybody. For those that want a free citation generator (not LaTeX-integrated though), please check out my newly developed APA/MLA, Chicago/Turabian machine. Take a quick tour, and if you like it (for example, its new scholarly discussion forum), bookmark it and keep in touch.

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Why don't you invest in Zotero, I use Zotero + Biblatex + Biber backend + TexStudio as workflow for automation of bibliography citations. You may want to have a look at my answer here, let me know if that works fine with you.

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“Why don't you invest in Zotero” – because nobody has convinced me yet that it would be beneficial. In particular, the website isn’t very forthcoming with information regarding BibLaTeX compliance. BibDesk stores entries in a .bib file internally and makes it effortless to fiddle with the acutual TeX. Does Zotero allow this? –  Konrad Rudolph May 18 '13 at 18:14
    
pressing CTRL+ALT+C is the only effort after setting up the workflow. Just give it a shot as described in the referred answer and I can help in case of difficulties. I didnt't try BibDesk I have to try BibDesk to better address your concerns. –  doctorate May 18 '13 at 18:19
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