Recommend me an app to organise my PDFs.

May 1, 2013 7:48 AM

I'm a PhD student and a typical day involves downloading and reading through lots of journal articles and eBooks. I store these locally on a MacBook. I am looking for something akin to the native Finder app, but which offers separate columns for "Author", "Title", "Year" and so on, as well as tags (very important). I have dabbled with Papers2 and Endnote, and a couple of "Finder"alternatives, but these either (A) duplicate the PDF files and save them elsewhere, or (B) don't offer the author/title/year etc. columns. Is there anything that will do what I'm looking for?
posted by FuckingAwesome to Computers & Internet (19 answers total)

The tool you want to use is Zotero. I know that it doesn't do exactly what you want it to, but once you start writing, you will find it to be completely invaluable, due to its easy integration with word processors and automatic bibliography creation.
posted by rockindata at 7:53 AM on May 1, 2013 [4 favorites]

Bibdesk and Mendeley spring to mind as possible alternatives to Papers and Endnote. BibDesk is free. It's geared toward use with BibTeX/LaTeX, but you can ignore that functionality and just use it to catalogue your PDF library. Mendeley is owned by Elsevier, which means you should boycott it, and my experience with it before the Elsevier buyout was not good, but throwing it out there.

Why is it a problem that these apps rename/move the files? Assuming the metadata is good, a computer program will generally do a better job than a person of organizing them, which is tedious and error-prone. E.g. I have Bibdesk set up to file all my PDFs in ../Bib/Author/AuthorYYYY Title.pdf. Better than the cryptic telephone number names they have when I download them.
posted by caek at 7:55 AM on May 1, 2013 [1 favorite]

Some apps you could look at to see if they meet your needs:
Yojimbo
Devonthink
Together
EagleFiler
posted by bluecore at 8:00 AM on May 1, 2013 [1 favorite]

I'm in quite a similar boat, and I use Papers2. I don't have a problem with the file-moving, but if you go to Preferences>Library, you can uncheck two settings "Copy files to Papers library folder upon import" and "Delete original file upon successful import". I think this should allow you to maintain your papers in whatever structure you'd like to.
posted by Maecenas at 8:11 AM on May 1, 2013 [4 favorites]

Spotlight and Finder kind-of already do these things. Spotlight advanced search can find documents by author, then you can create smart folders to virtually organize your files, all without rearranging them.

Rigid folder hierarchies are an anachronism. A big ol' heap of files works better in these days of cheap indexing power.
posted by scruss at 8:17 AM on May 1, 2013 [1 favorite]

I've played around with various reference management software and in the end I keep coming back to Bookends. The default behavior for PDF files is that it will link to them wherever you've saved them, but you can also specify whether you want them moved elsewhere. In practice I've found it convenient to have them all collected in one folder. The "Keywords" field functions as tags, from which the program can display a tag cloud.

There is a separate iOS app called Bookends on Tap, which I have found convenient for reading journal articles on an iPad, for when I'm on the move or I'm working on a computer that's not my main mac.
posted by research monkey at 8:24 AM on May 1, 2013

I am a Ph.D student and I love BibDesk for this purpose. I have it configured to automatically move/organize pdfs, and since I publish in LaTeX, it makes my life very easy.
posted by Alterscape at 8:28 AM on May 1, 2013

I, too, use Zotero with the Zotfile add-on. It will link to the pdfs where you store them or you can use its own database to store them. If you just choose to link (which is what I do -- no duplicate copies), Zotero can also automatically rename the files something sensible according to whatever metadata you prefer. It has columns for all the usual bibliographic things -- I don't know if the tags show up in a column, but you can do other types of organization with the tags which may be helpful.
posted by bluefly at 8:30 AM on May 1, 2013 [2 favorites]

I use Papers for this purpose exactly. The one nice bit of software not mentioned so far is Sente, which I think also has the option to not reorganise the PDFs.
posted by roofus at 8:51 AM on May 1, 2013

I use BibDesk.
posted by leahwrenn at 9:19 AM on May 1, 2013

Zotero with the Zotfile add-on is pretty great.
posted by medusa at 9:23 AM on May 1, 2013

Another vote for Sente. I tried lots of these options, but Sente was the only one that scaled up to fit my library, was stable, and knew how to do cross platform syncing in an intuitive and elegant way.
posted by R. Schlock at 9:33 AM on May 1, 2013

Came to recommend Zotero.
posted by Emperor SnooKloze at 9:34 AM on May 1, 2013

Any of the major reference managers will work. I like Zotero, but a lot of my Mac-using colleagues like Papers. I'll point out that you're not quite asking the right question. All of these tools keep track of all the metadata for each citation (author, year, publication, etc), have ways of keeping notes and annotations, categorizing and tagging references, and other tools to let you maintain and organize a library. Many of them have browser integration add-ons that will scrape all the metadata, download the pdf, and add it to your library with one click. And especially, they all have ways of managing document citations and generating bibliographies. You need all of these features, even if you don't know it yet!

Also, cloud integration and backups, also included in many of these apps. If you store your reference library locally in one place you are asking for it to disappear in 3 or 4 years when your hard drive fails, right when you need it most. Don't be one of those people, please.
posted by PercussivePaul at 10:32 AM on May 1, 2013 [1 favorite]

Calibre is free and will do all of what you are asking. You can customize tags, etc.
posted by mazienh at 10:52 AM on May 1, 2013

Mendeley does this! I just checked. (I hated Calibre.)
posted by lokta at 11:14 AM on May 1, 2013

Mendeley is great and does just what you want (and more).
posted by Midnight Rambler at 9:02 PM on May 1, 2013

FYI - I wouldn't get too attached to Mendeley. It was recently purchased by Elsevier and they might be inclined to change it in ways that aren't too useful for its current users.
posted by barnone at 10:23 AM on May 3, 2013 [1 favorite]

Seconding Calibre. It is the management program for ebooks, handles PDFs as well as every ebook format in existence, and has plenty of other features. The developer is very responsive, and there are updates to the Windows version something like once a week. I don't have a Mac, so I can't tell you the update schedule for that.
posted by timepiece at 5:36 PM on May 3, 2013