Papers : you know, to organize ’em

I ponied up the money and bought Papers recently — it’s not perfect but it does let me store all of those pesky PDFs I have lying around in a convenient single location.

The program acts like “iTunes for your papers.” It has its own internal storage system (which is also customizable) and lets you create collections (e.g. playlists). The best feature is the interface to various repositories such as PubMed, ArXiV, JSTOR, ACM, and Web of Science. It technically lets you search IEEEXplore as well, but IEEE just upgraded their system (color me unimpressed), which broke the current version of Papers’ search interface. I’m sure it will get fixed soon enough.

What I wish it let you do was to tag papers so that you can click on a tag to see all papers tagged with that topic; while this functionality is there, it’s not transparent to do it. I’d also like it if the BibTeX was associated as metadata with the paper file, so that I could integrate it better with BibDesk. I had contemplated getting DEVONthink to organize all of my files, but I felt like that was overkill.

Does anyone else out there have a killer system for organizing papers? I know it’s just a crazy dream that I’ll actually get a chance to read most of the papers I have sitting on my hard drive, but I’ll be more likely to read ’em if I can find ’em.


14 thoughts on “Papers : you know, to organize ’em

  1. Does anyone else out there have a killer system for organizing papers?

    Ha ha, I’ve heard this question asked in person at parties, I’ve seen it posted in grad student/academic forums online, I’ve asked other people in my department… It truly seems like NOBODY can actually say yes.

    I have Papers, and it has some great stuff – like auto-matching via google scholar, and searching the databases, and automatically showing you the latest & greatest from journals you already have stuff from.

    The main problem I have is keeping it updated. Unless I manage to get myself into the habit of always choosing “Open with Papers” every time I d/l an article, rather than saving it or opening it in the default Preview, I wind up with piles of new PDFs that need to be moved over to Papers. And I wind up finding myself using Spotlight to find anything, as though Papers didn’t exist.

    I’m finally going through and adding keywords to everything (I didn’t even see that it had them at first, I thought you had to use the damn Collections), which will make it more useful than Spotlight for searching finally.

    • The initial cost of tagging with keywords seems not worth it unless you are going to look at those papers actively (like tag as you go along, or tag-and-release…)

      I basically do all my searching, like JDO, via Papers now. It’s more or less awesome.

  2. Also, I have seen a few posts here and there about combining Papers with Zotero, which seems to hit most of the things Papers misses, like including non-journal-articles (chapters, etc) and inserting citations automatically. But I have a hard enough time keeping ONE system up and running, I don’t know when I’ll get around to setting up TWO!

    • yeah i know people who use zotero but i think that the fields I work in operate via the Least Publishable Unit (LPU) an so Papers is sufficient to keep track of most of it.

      I heard DEVONthink integrates well with Papers but I am on a budget and all.

  3. I’ve never used Papers (Linux), but I’ve been really enjoying Mendeley. Biggest draws for me were the embedded annotating PDF reader, online shared collections (so I can share both papers and our aggregate annotations with collaborators), and the fact that it’s free. The online features seem interesting, haven’t given them much of a whirl yet. Let me know if you give it a try!

    • Wow, Mendeley looks pretty awesome too, and now I wonder if I wasted my money on papers. I think the embedded search in Papers outweighs the paper sharing in Mendeley (since I don’t have the kind of collaborations which need a shared library).

  4. oh and – my biggest problem right now is filtering the stream of papers that come out in my field. Right now my cutting-edge solution is to use gmail labels to mark emailed journal TOCs that trigger keywords of interest. I’d love to do something a bit more narrow, but I can tolerate a lot of false positives towards the goal of minimizing false negatives.

    • I think there aren’t as many papers coming out that I need to look at — since journal publication is so slow, it’s all about ArXiV for me, and there aren’t usually that many coming out there.

  5. I put them all in a single directory, so I’d say that’s a “no.” But:

    It technically lets you search IEEEXplore as well, but IEEE just upgraded their system (color me unimpressed)

    Me too! Why do websites always figure they have to completely change everything around every couple of years for no apparent reason. (That’s how some non-technical publications of mine got lost down the memory hole.) This new system stinks. Not only do you have to both scroll and click five times to see an issue, but you can’t open in another tab. It’s a very frustrating way to look through an issue.

  6. I also use Papers and have liked it a lot. When I started using it several years ago, I sent them a whole pile of suggestions for their BibTeX support, which they’ve indicated they have on their plate (but clearly not a high priority).

    For me, just the “search” feature is worth the money. I’ve tagged some papers, but searching generally works just fine.

    I also get annoyed when search-web-site compatibility breaks.

  7. Also, update your search engines by going to Preferences, Plugins, Search Engines and double-clicking on the ones with updates. Works like a charm!

  8. i love “sciplore mind mapping”. on youtube there is a great video showing what this tool is supposed to do

    although the current beta cannot do everything shown in the video, THIS really is how i want to organize my papers

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