Help me organize research
September 13, 2009 10:26 AM   Subscribe

Zotero, Scrapbook, Papers, Evernote, etc. What should I be using to best organize materials for a research paper?

There are lots of research organization software/browser plug-ins available now, and trying to make sense of which to use (whether standalone or in conjunction) is giving me a headache. I'd like to be able to take notes alongside either text from websites or PDFs, store, sort, and view PDFs, create citations/bibliographies, etc. Which of these and/or other tools will help me do that?
posted by rbf1138 to Education (15 answers total) 52 users marked this as a favorite
About to start the third year of my PhD - and I've tried various methods (including endnote and a wiki). I now use a combination of evernote and zotero. I use evernote to take notes, put in details of what was discussed at my supervisor meetings, to take pictures of the front pages of books I'm taking notes from, and often just to snap a particular passage using my cell phone.

The most important thing to remember is that what you want is a) ease of use and b) back up. I would suggest portable firefox with zotero application on a flash drive you regularly back up. For note taking, evernote - to which you could occassionally copy in your running bibliography as a further safety measure. Back up, back up, back up. Oh... and do it as you go along....
posted by Augenblick at 10:35 AM on September 13, 2009 [1 favorite]

Zotero is pretty sweet. If you're on a Mac, however, I'd recommend Sente. It's got many of the best features of EndNote, Papers, and Zotero rolled up in to one package. It's easy to navigate and organize your own library, has great cite-while-you-write functionality, and you can even set it up to pull down new relevant articles based on whatever criteria you select.
posted by solipsophistocracy at 10:56 AM on September 13, 2009 [1 favorite]

I use Scrivener for writing papers. You can import pdfs as well as clippings from webpages. You can use endnote's temporary citations, and then when exported to Word or something, they can then be converted to proper citations and build a bibliography.
I also use papers, but this is more to keep track of the papers I have in my library. During the actual writing process, I tend to use Endnote more.
So basically Scrivener for writing, and storing things like graphs and tables, or even stats results in the same file, endnote for references, papers to keep track of the pdfs.
posted by dhruva at 10:58 AM on September 13, 2009 [2 favorites]

Response by poster: ^^ Should have noted that yes, I'm on a Mac.
posted by rbf1138 at 11:05 AM on September 13, 2009

Seconding Zotero, primarily for its portability. I work on a lot of different boxes running all three major OSes and Zotero works on all of them. Now that it backs up and syncs your cites, it's even better in that respect.
posted by alphagator at 11:17 AM on September 13, 2009

I'm one of the minority who really don't like Zotero. I find it to be okay if I want to just quickly mark something as "to read" by collecting it into the database but anything beyond that I have had troubles with. It often mis-collects important information and I've had more trouble producing bibliographies with it than I'd like. Plus, the way it deals with notes and the way I use notes don't really jibe. It is worth a try, though. As this AskMe suggests, enough people love it that you should see if you do, too.

I'm currently going through my annual reconsideration of how I do organize my research, mainly because I'm all over the place. I have notebooks in which I take notes from meetings with my committee members, ideas that strike me, quick outlines, and notes form some books—sometimes I do like to be able to work without my computer—and I also have two huge text files that are each just notes on primary and secondary sources I'm working with. I assemble a bibliography in Endnote and then copy and paste these notes (which I take using Writeroom, mainly) into the Endnote database for future reference.

I think the most important thing is that it is something you'll actually use consistently. Being a disorganized mess like I am recently has made it a huge pain when I need to find anything. Try to be consistent in how you collect and keep your data and you'll do fine.
posted by synecdoche at 11:25 AM on September 13, 2009

I don't really care for zotero either. I'd recommend Papers. Or if you're looking for a great note-taking application with pdf import/export capability, I'd also recommend Circus Ponies' Notebook.
posted by handabear at 12:06 PM on September 13, 2009 [1 favorite]

Having just started graduate studies for my Ph.D., I was in the same bind and I looked at all the options mentioned, finding that nothing really worked the way I wanted it to. Then I stumbled across Mendeley, which has really simplified my literature management.

Mendeley allows you to easily index and automatically organize papers based on the hierarchy you select. It will extract author names, titles, journals, etc., and will also pull information off the web based on the doi/issn numbers of each paper. You can search through the full text of all your papers to find something you're looking for and it has a nice built-in PDF viewer to immediately show you results. You can store notes on each document, and the best part is that you can sync everything (including PDF files) to the web, where your colleagues can view them. It will also allow you to copy and/or export citations in any of the common formats (APA, MLA, Chicago, etc.).

I'd highly recommend you look at it--the program's still in development and so it has some bugs, but I've been using it successfully for almost 6 months and wouldn't consider switching to anything else. It's available on all the platforms commonly encountered in research: OSX, Windows, and Linux. Oh, and unlike EndNote, it's free.
posted by Aanidaani at 12:30 PM on September 13, 2009 [3 favorites]

I love Microsoft One Note (I'm not sure if it's available on a Mac though. I tried Evernote and found it really lacking in functionality.
posted by kylej at 1:59 PM on September 13, 2009

I use a combination of Evernote and Scrivener - I prefer Scrivener, but needed a note taking solution on my iPhone. It's worth noting that Scrivener can now import from WriteRoom on the iPhone, which is handy too. The ability to float a scrapbook above my browsing windows and drag snippets of text, URLs and images to it, to organize web pages and text and video together in a single organized document - well, I've been using Scrivener since 2007 and I adore it and recommend it everywhere. It does everything I can think of, including giving me the ability to store meta information about notes.
posted by annathea at 4:23 PM on September 13, 2009

Thanks for the Mendeley recommendation!
posted by proj at 4:41 PM on September 13, 2009

To piggyback: I just got Mendeley, which looks really great. It's not doing the greatest job, though, of detecting all the author/title information from my articles, many of which have a JSTOR cover page that seems like it would be about as easy as it gets to distract from.

When I tell it to search by title, it still doesn't find anything, even with papers with very long, article-specific titles that I've entered in the title field. Any ideas?
posted by nosila at 5:56 PM on September 13, 2009

Response by poster: Late addition: will any of these help with in-text citations? Do I then need to use something like Refworks in conjunction with Zotero/Evernote, etc. for that? Sorry to not have mentioned this in the original question.
posted by rbf1138 at 12:01 PM on September 14, 2009

rbf1138, Endnote will do in-text citations in conjunction with Word.
posted by synecdoche at 4:59 PM on September 14, 2009

Mendeley also includes a plug-in that will allow you to easily work with citations in Word.
posted by Aanidaani at 6:14 PM on September 14, 2009

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