Help me find an academic paper management program

November 19, 2011 11:51 AM

I'm having trouble finding an academic paper management system that meets my requirements (Mac+Win, BibTeX, automatic PDF filing, easy to import etc).

I'm a PhD student studying remote sensing (basically scientific satellite imaging), and am having trouble finding a bit of software to organise my journal papers and references. So far I have been keeping PDF files randomly spread around my hard drive, with references imported into BibDesk from the BibTeX data on Google Scholar. However...this isn't really working, and I now need to be able to use both Mac and Windows.

So, I have a number of requirements - but nothing I've really found seems to fulfil all of them:

1. Must work on OS X and Windows
2. Must produce one automatically-updated BibTeX file with all of my references in it which I can use in LaTeX
3. Must automatically file PDFs with sensible names (Author_Date_Title.pdf for example)
4. Must be easy to import references and PDFs to (either from browser extension, internal browser or something)

The last one seems to be the hardest to find - so many programs will import just the reference details, and leave you to find the PDF file. Similarly, other program (like Mendeley) will let you import the PDF file, but then screw up getting the metadata from it. Is there anything that will easily import metadata and PDFs for most references via a simple browser extension or similar? I find it strange that most software can't even do the simple task of searching on Google Scholar for the article title and downloading the PDF (as PDFs on Google Scholar often don't require authentication as they are on authors personal websites).

Any advice or guidance would be great. I've tried various bits of software, and read about many more, but have never quite found something that does it all.

posted by robintw to computers & internet (8 answers total)

It doesn't meet all of your requirements by any means, but Papers is pretty sweet.
posted by killdevil at 11:58 AM on November 19, 2011

Nope, I don't think anything out there meets all your requirements. But Zotero meets requirements 1 and 2, makes it easy though not completely automatic, and meets part of #4 - will definitely import both references and PDFs, has some PDF metadata tools, but usually won't fetch the PDF for you.

You should try it. It is open-source, free, and if you know anything about programming, you can, without too much trouble, alter your most commonly used sources so that they download the PDF too (then you should turn around and upload your contribution back to the community).
posted by shivohum at 12:07 PM on November 19, 2011 [1 favorite]

The most recent versions of zotero have done a better job of snagging the PDF from various sources when I am capturing the bibliographic information. There is also an add-on for zotero called ZotFile which will rename the downloaded PDF file so 123456.pdf becomes Smith_2010_How-Children-Learn.pdf. So even in cases where the scraping of the PDF is not automatic, the alternative is a two step capture and rename process all within the program. I really committed to using it when I found zotfile because it allowed me to systematically rename a few hundred papers already on my hard drive.

It does export to BibTex, but that is not my thing so I can't comment on whether or not it does it well. It runs as a browser plugin and they just released a standalone version, though I have not tried it out because I am superstitious about it "converting" my database.

On preview, what shivohum said noting that zotfile takes care of need #3.
posted by cgk at 12:11 PM on November 19, 2011

Two pieces of software you should check out:

Zotero - great for reference tracking, building bibliographies

mendeley - kind of like an iTunes for PDFs and references

I use Zotero everyday
posted by 0bvious at 12:12 PM on November 19, 2011

Mendeley and Zotero are the best we have. Frustratingly enough, they are way better than what came before. This is an area where it seems like the solutions would be easy to code up, but in practice they seem to be quite difficult.

This means that you are highly unlikely to see good software that does it all. It's a problem that seems easy but is hard, marketed to poor people (grad students) with high standards. There is very little upside. I recommend Mendeley - if their auto-import is getting borked on something, let them know. They seem very responsive on Twitter, etc.
posted by pmb at 12:19 PM on November 19, 2011

This doesn't solve the bibliographic problem, but there is no reason you can't just sort your PDFs yourself. I keep my secondary sources (PDFs, notes) in a single folder, sorted alphabetically by name of first author and date. So if I was to read Overton (1998), I know right where to find it. tagging or keywords can then be done in your bibliographic software; the PDFs just sit in a simple personal library.
posted by jb at 8:30 PM on November 19, 2011

If you're open to web-based solutions, citeulike does about everything you're looking for.

It can import and export BibTeX files, and can export a subset of papers based on tags. You can easily add new entries using a bookmarklet, and for the few journals or gray literature that don't work w/ the bookmarklet, you can always grab the BibTeX link from Google Scholar.

As far as attaching PDFs, you can either upload them manually, or if you have an academic library connection, you can run SyncUThink on your account, and it will go through your citeulike library, search for any missing PDFs, and attach them. Oh, and you can also use SyncUThink to backup your library from citeulike. It will save the references out to a BibTeX file, and download the PDFs into folders.
posted by indeterminacy at 1:32 AM on November 20, 2011

Meet with a Subject Librarian of your college. They might have good options. Sometimes libraries purchase products like these.
posted by WizKid at 1:43 PM on November 22, 2011