Reference Management Apps


Philosophers, I have been asked to ask you all about reference manager / bibliographic software, such as Endnote, Qiqqa, Mendeley, Zotero, etc. Do you use any of these? Is there one in particular you would recommend?

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Elmarie
Elmarie
6 years ago

Mendelay is quite good. I use it to store all my files because you can search keywords in pdf documents (something windows doesn’t allow you to do unless you open the file). I still prefer to manually enter my citations though. I find the formatting that these programs impose aren’t always aesthetically satisfactory.Report

Kris McDaniel
Kris McDaniel
6 years ago

I’m more a reference magnet kind of guy.Report

Dennis
Dennis
6 years ago

The BibTeX tool that comes with MacTeX (the TeX distribution for mac), BibDesk, is pretty neat. It’s mainly worth it if you are gonna be using LaTeX and BibTeX, but it can export to any citation style in plain text, RTF, HTML, and RSS. So, it should be useful for even non-LaTeX users.

Check out the wikipedia page .

Benefits of BibDesk:
1. Open source.
2. Their file format (.bib) can be read by any text editor, so even if 20 years down the line BibDesk is no more, you can still recover (albeit tediously) your citation database.
3. Can import citations from many websites like journal publishers and PhilPapers (“export to BibTeX”, then copy and paste, then have BibDesk “Add from clipboard”).
4. When used along with BibTeX in a LaTeX document, produces well-formatted citations (I haven’t tried to export to other formats, but I’d be surprised if they were shoddy).
5. Lightweight. (I found Mendeley a bit too clunky and featureful in my [admittedly limited] use of it; to repurpose an old emacs jokes, “Mendeley is a great operating system, lacking only a decent reference manager”)

Downsides
1. Not a commercial app, so not a huge development team.
2. No mobile app (though for me that’s not a big deal; and for all I know their is some other decent BibTeX app for mobile).
3. Not the prettiest interface.Report

Greg
Greg
6 years ago

If you use LibreOffice for word processing, then Zotero is great (I can’t speak to its quality when paired with Word). It’s free, easy to use, and as far as I can tell, bug free. The desktop client also runs great on Linux, if you’re into that.
I initially tried to use Mendeley, but discovered (fairly quickly) that it doesn’t allow you to include page numbers in your citations (!), at least not with the LibreOffice plugin. The developers may have since fixed it, but if not, that’s a pretty huge limitation.Report

shane
6 years ago

Another vote for Bibdesk. It also syncs with dropbox, so you can have your repository of automagically filed and tagged pdfs sync across your home and office machines.Report

Jeff Y
Jeff Y
6 years ago

I’ve been using zotero with word for a few years now. It’s free, easy to add references (e.g. via google scholar and a browser plugin), and pretty easy to add in-line citations and create bibliographies in word. It’s actively maintained and updated fairly regularly. It does not play quite as nicely with bibtex in my experience, though I have not mastered all its features.Report

Matt
Matt
6 years ago

Here’s a third for BibDesk. I agree with everything that’s been said about it above. But here’s another reason to like it: You can set it up to display (and search/filter) your notes and annotations from Skim (a great free PDF reader for OSX) when you are looking at a bibliographic entry. I find this to be really, really helpful for finding things in my notes later on.
You can accomplish this using the “preview template” available here: http://jhh.med.virginia.edu/main/TemplateNotes#otherTemplatesReport

Andrew
Andrew
6 years ago

Does anybody know of a good reference app for Android? I use Endnote on my desktop and like it, but unfortunately there’s no official app for it on Android (though apparently on iOS).Report

Matt
Matt
6 years ago

Oh, and here’s another good thing about BibDesk that hasn’t yet been mentioned. One drawback of BibDesk is that it doesn’t really have a good native way to automatically import bibliographic information like Zotero does. Zotero is really good at scraping bibliographic information from websites (e.g. JStor, PhilPapers, Google Books, etc.) and BibDesk doesn’t really work as well for that. However, there is a Firefox plugin called Zot2Bib ( http://mackerron.com/zot2bib/ ) that automatically copies new zotero references to your Bibdesk library. So, you can use the metadata scraping power of Zotero from within Firefox to automatically create new entries in Bibdesk. Effectively, that is, you get to co-opt Zotero’s best feature for use in BibDesk.Report

FM
FM
6 years ago

Anyone have experience integrating any of these reference managers with Scrivener?Report

Glenn Carruthers
Glenn Carruthers
6 years ago

I recently switched from endnote to Zotero. I’ve found Zotero to be much more stable and it’s import references from websites is much much better than endnote. Generally it’s more intuitive as well, only downside is that modifying the output styles is quite fiddly.Report

Alex
Alex
6 years ago

I’ve always been using Zotero, which I think is great for getting references of the internet and managing them, but (in my experience) slightly less great (but still mostly very good) for putting references into documents (into lyx through an extension called lyz in my case — and I think that’s part of the issue).

Funnily I was just researching reference manager software when seeing this post. I just discovered something called “colwiz”, which I have never tried, but which looks like it might be good (has apps for multiple platforms like Zotero, including a web app, which I think maybe Zotero doesn’t have, and seems to be quite actively developed). I’d love to know if anyone has tried it and has an opinion about it.Report

Peter
Peter
6 years ago

Having at various times tried various options, from early versions of EndNote onwards, BibDesk is a clear winner — it “just works” in an extremely stable, predictable way. And since the biblio data is just a text file in a format with a huge user base, your data is future-proofed.Report

Jonathan Weisberg
Jonathan Weisberg
6 years ago

BibDeskers: after years with BibDesk I’ve just started to stray, seeking an alternative that can seamlessly import both a PDF and its bibliographic data. (I’m currently trying Papers, with mixed results.) Is there a way to do this in BibDesk?? Sounds like maybe others know something I don’t… or maybe others just don’t expect this functionality?Report

Jeff Y
Jeff Y
6 years ago

These comments are making me consider trying BibDesk. Has anyone tried integrating BibDesk with Word (which I am often forced to use)? I see there is something called BibFuse that is supposed to facilitate this. Anyone have any experience with it?Report

Dennis
Dennis
6 years ago

Justin:

You can drag PDFs to BibDesk and use it to store them like a database. This post suggests that BibDesk does import PDF metadata, but I haven’t been able to get that supposed feature to work. The post does contain a lot of useful tips for how to import reference data, though.

I find it easy enough to import the info from PhilPapers or one of the other online methods (Publisher, Google Scholar, etc.) that I don’t really miss PDF metadata import. Add to that the fact that, in my experience, PDF metadata is pretty spotty and incomplete at best (so much so that I wouldn’t trust that without verifying on the publisher’s page; but if I’m there then I can just import the citation directly to BibDesk).Report

Oliver
Oliver
6 years ago

Apparently yes: , but I’ve not yet taken the trouble to try to emulate what he’s done. This summer I dumped Papers2 for BibDesk, both because Papers was bought by Springer, and because the Papers3 release seemed like a disaster. I don’t regret it.Report

Oliver
Oliver
6 years ago

Pocketbib is a very good bibdesk-friendly mobile app.Report

Oliver
Oliver
6 years ago

The link in my post went missing. It was to this youtube video.Report

David McNaughton
David McNaughton
6 years ago

The above discussion is rather intimidating to an old fogey. I use Word and I get p.o.’ed with different presses wanting bibliographical entries in different styles. I want a very simple program that allows me to go from Oxford, to Cambridge, to Harvard etc.Report

Sergio Tenenbaum
Sergio Tenenbaum
6 years ago

David, I think that Endnote is the best option for the non-techie philosopher. Endnote comes with all the features that techies hate: it is proprietary software; it’s expensive and it will force you to upgrade any time you upgrade Word; it does not play nice with LaTex and Markdown (at least this used to be the case; I don’t know now); it can be buggy at times, and you can’t fix it on your own. But for the total non-techie working with Word is probably ideal: it is very user-friendly, and it also has a very helpful customer support helpline that you can phone in (or so I am told, see below). Moreover, it has an extension for Word that allows you to cite as you write (though at least on a Mac, the extension has a number of shortcomings). You should know that it pains me to write all this. I am nowhere in the same league as the people above, but I am proudly Endnote-clean for almost three years now. And I’d rather give up publishing philosophy than telephone a software help line.Report

Erik Angner
6 years ago

I have experience with BibTex, EndNote, and Zotero and Zotero is by far the most stable and intuitive. The integration with Word works fine, it syncs over the cloud, and allows you to upload and organize pdfs as well. Obviously, it’s free. The one annoyance I’ve noticed is that it slows down when documents are book-length manuscripts, but you can speed it up a bit by turning off the automatic pagination in the Word preference pane. Disclaimer: I’m employed by the institution that developed Zotero, but have no other relationship with that team.Report