Ask Science Woman: How do I organize journal articles?

Another from the archives (originally published February 6, 2006).

Let it not be said that I don't respond to readers' comments. A few posts ago, I was moaning about my inability to read journal articles in an efficient and non-fattening way. Yami requested that I share my system for organizing journal articles, writing that "Curious people who are finally getting quasi-permanent office assignments and file cabinets want to know."

The succint answer: Invest in a copy of EndNote or similar and a thick stack of file folders. As soon after downloading/copying/printing a journal article, add it to your EndNote library. For paper articles, create a manila folder for each 1st author. For PDFs, name them by authors, year, and any other identifying info (subject? journal?) and put them in a folder by letter of the alphabet.

The rationale: I've tried other methods (subject folders, general letter of alphabet folders, by class, by journal (the worst!)) and all have dissapointed me or become too cumbersome. This method takes me a little bit of effort up-front but is much easier to use in the long run.

The details:
We've all seen the professors whose offices are overflowing with stacks of papers and books...don't become one of them. Start using a system as soon as possible in grad school, because it will be hell to catch up with the backlogged paper buildup if you don't.

In Endnote, use one of the superfluous headings (I use "notes") to designate whether the article is paper or electronic, if it was assigned for a class, or if it is filed someplace weird.

I started with multiple end-note libraries. One for thesis, one for -ology #1, one for ology #2...and these were keyed to certain drawers in my file cabinent. Lately I've just been adding everything to my thesis library (and drawer), rationalizing that it won't make sense to keep my thesis papers separate once I'm done with my Ph.D. The jury's still out on this one though. I'm starting to think it will make it harder for me to find pure-thesis papers as it get into the final throes of writing.

If you have a lot of papers by a single author, divide them by subject or year, whatever you can clearly label or delineate.

In a few cases, I've lumped a paper with a terminal M.S. students first author into the folder with their advisor's papers. But I always make sure to note it in endnote.

When I'm feeling really overwhelmed and just don't have to deal with new acquisitions, I put them in a designated place until I can get at them. That way I always know what's been endnoted and what still needs to be done. No point hanging on to a PDF or paper if you are never going to recall you have it.

If you have a PDF, you can cut and past the abstract/keywords into endnote. This will make searching your library easier later on. If there are keywords that the authors didn't include, but that I might find helpful for categorizing a paper, I'll add them.

Some journal sites and databases will import references directly into Endnote for you. This is a time saver, but one caveat...think really hard about importing a reference for a paper you don't yet have. I remember how frustrated Writer Chica got during her M.S., because she could never figure out which papers she had and which were only references she had meant to get.

This kind of feels like an ad for a software product, but I honestly can't imagine scholarly life or graduate school without it.

Got a question for me(and my infinitely wiser readers). Send an email to: science (dot) woman (at) gmail (dot) com.

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Zotero is a new product that is similar to EndNote but it has the advantages of being free, open source and way easier to use. It's not perfect but I think the advantages out weight the disadvantages at this point in time.

I used the same strategy with smug success for years, back when articles were things you photocopied, but never properly made the switch to pdfs. I abandoned EndNote after the very nasty experience of updating to EndNote 8 without first reading the reviews - we now use the Mac-specific BookEnds instead. (BookEnds is great with pdfs.)

But I'm now old enough and forgetful enough that having to look through a stack of printed-out pdfs to find the paper I want is an advantage - it reminds me of all the other papers I decided were too important to throw out.

I remember getting paid by my dad when I was younger to file papers in his big filing cabinets (I got paid by the paper), and also filling out those little cards you used to have to send to get copies of papers.

I use RefWorks, which I have for my full-time job as well as my part-time adjunct teaching gig, and so have 2 distinct accounts. I am training myself to export article citations to RefWorks when I find them and file them into relevant folders. I've created a folder of citations for a student doing work on a difficult-to-research (even for a librarian) topic, and I've created one for my publications. In my teaching account, I have folders for the two different classes I teach.

RefWorks' weakness is the inability to tag / difficulty in creating notes. I'm so used to tagging that I want to be able to do that quickly everywhere. Its strength is that citations are embedded with my institution�s "OpenURL resolver" which means that I can easily get to the full-text of the article if it's online anywhere. This means I've stopped saving the pdfs.

Not sure how this will work as a long-term solution, but for now, it's pretty good.

Many library databases (PsycINFO, Web of Science, Scopus, "pay" Medline via library vendors) make it really really easy to export to RefWorks and endnote. Sadly, they don't support the terrific free Zotero that John recommends, but that's available as a nifty free plugin for FireFox (Mac & PC).

Why oh why are you printing them out????
For my PhD and teaching I keep a separate hard drive on which any pdf docs I need are kept, I also have a copy of MS OneNote, and EndNote on my main computer.
I put all the refs into EndNote, and mark in the comments area if I have a copy of it or not (sometimes!!).
I save all pdf docs, under name and year, on the hard drive.
Then as I work through them I cut'n'paste from pdf to OneNote to make comments. Cool stuff!
I haven't tried Zotero - but hey, anything open source has to be getting better all the time!

Nice post, and a great service to academia. I use a very similar system with a few differences, described here.

I use a similar system - save everything by first author and year on hard drive then import the PDF file into endnote (the newest version). As for paper copies (and I know I'm bad for suggesting this, fair use and all but one digital copy, not for distribution) but if you photocopy on some copiers you can digitize the file as a PDF. As I'm moving back to the UK I'm trying to cut back on paper. I've so far done this for all my payslips, bank statements and other life related paperwork, but it could be applied here.

Science Woman, I finally accepted your invitation! Many thanks.

As for this topic I use Procite, mostly because it's what I'm most familiar with. However, I don't bother with alphabatizing, I simply put a number on the top of each paper and put that number in as it's library location. This way I don't have to constantly expand certain alphabet sections and I simply file them by number. It makes everything easy to find even if they aren't grouped and it also means everything gets filed promptly. When possibly I just keep the PDF's which I also name by numbers but with the letters CD in front of them so I know it's electronic. I copy the same document in twice if I have both a hard copy and a electronic so I can put both "library" positions in. I put all of my PDF's in one folder on my hard drive and back them up to CD's labed by the numbers they contain. I also keep my notes for the papers in with the Procite file so I can remember what I thought was most relevant to me.

I've adopted Science Woman's system, and it hasn't failed me yet. I use BibDesk (Mac-only) instead of EndNote, though - infinite custom fields for notes and keywords, plus it works with LaTeX and files my PDFs for me.

Sounds like a good system! I use something similar that was started based on the suggestions in a great book on grad school that I read last year, Getting What You Came For. The difference for me is that, like Bronnie and others, I do it mostly digitally. I do store some that I have physical copies of in a pretty similar manner, though. Also, I use Myendnote on the web, which is linked with Web of Science.

If you do separate end note files for what you have, what you need, and what is on order, then you know the status of all the papers you are looking for. This is especially important if you need to order lots of things via interlibrary loan or from obscure overseas publishers, and it takes months to get them.

I have already completed my thesis-writing for my M.Sc. and needless to say, I have my journals and printed papers in various files and they are as unorganized as my room!

I have heard of EndNote ealier but it is expensive (especially if you have to multiply the USD to 3.5 into my local Malaysian currency!) hence I had to settle with box files and ring files and cloth bags!

But I will definitely try Zotero (thanks, John for mentioning it) and see if it could help me, especially since I am planning to do my Ph.D. this year :D

I never print anything out any more. It is simply too difficult for me to keep track of paper copies of stuff. If I can't get something in electronic format it is so much less useful to me that I mostly don't bother. In electronic format I can take everything with me on my laptop. There are few papers that are so unique that they are "must haves" and are not available electronically. There is enough redundancy in the literature that once you have "enough", you don't need to get everything.

I don't use a special filing program, just give each file a name, usually the first part of the paper title. I use google desktop search to keep track in a way that is redundant to my idiosyncratic filing system. I use to save copies in multiple files for easier searching, but that takes up too much space so I don't do that any more.

This way, most of the papers that are about "the same" things are together, so I can look at each one as quickly as it can be brought up.

But this is what works for me, and might not be suitable for anyone else.

I am also done (mostly) with hard copies. I have a tablet PC now and read/annotate PDFs right on it, and then save the annotated version as a separate file (with a coding system, of course). Tablets and digital readers are getting better and better at replicating the "real" experience. In addition, the number of papers that I used to not be able to find digitally keeps dwindling...although there will always be some that are too obscure. In that case, if I find myself looking at the hard copy for some reason, I go ahead and take a little time to scan it to PDF. Collaborators of mine do the same, so there is potential to share. I very much like the thought of being paper-less. What a waste.

Finally...I name the PDFs similar to what's described above, and then use GoogleDesktop to find them...which works pretty well.