Zotero Zorros, share your techniques.

June 5, 2009 8:32 AM

How can I optimize my use of Zotero?

I've got a box with several hundred journal articles in it. Most of them have obscene amounts of highlighting and notes written directly on the article or on paper stapled to it. I'm moving across the country to start grad school in a month, and I've realized that hauling all this paper with me is not going to be an effective strategy. That said, all the PhD advice I read says to organize your library early and often, so I'm taking this time to digitize the all the science I've been studying for the past year or so.

After lengthy debate between EndNote and Zotero, I've decided to go with Zotero, and have begun collection citations, tagging articles, making notes, etc. However, I feel like I'm not going about it in the most efficient way. I really like that you can have an item in more than one collection, but I'm stumped as to the best way to start organizing them.

What are your strategies for getting the most out of Zotero? I've also heard about using it in conjunction with bibTex, but I'm totally clueless on that front.

My degree will be in psychology, with a focus on developmental social neuroscience, but I'd love responses from anyone who has had to organize a large body of academic work.

posted by solipsophistocracy to Computers & Internet (12 answers total)

Mac or PC? If you are or will be using Mac, you might consider something like Skim (freeware), which will allow you to transfer the highlighting and notes directly onto the pdf, which you can then link directly to in zotero. It sounds laborious, but I've been doing it little by little and its not so bad, and there's something satisfying about dumping all that paper in the recycling bin. [And if you don't mind sinking a bit of cash into it, Papers ill help you grab and catalog the pdfs, though unfortunately it isn't yet integrated with zotero].
posted by googly at 8:41 AM on June 5, 2009 [1 favorite]

I think Papers is the way to go here. It's a fantastic program if you're on a Mac.
posted by proj at 8:45 AM on June 5, 2009

Response by poster: I'm on a Mac. Is Papers better for cataloging PDFs than Zotero? It seems easy enough to just attach them (or links to them, so I don't actually have to have all the PDFs on my hard drive). I'll definitely check out Skim in any case!
posted by solipsophistocracy at 9:13 AM on June 5, 2009

You're right, it is easy to just attach links to pdfs through zotero (you can also create snapshots where html views are available). But that only works if you are using a computer that allows you online access to those pdfs.

The main advantages of Papers are:

(1) You can set it up to automatically rename any pdf that you download or add to your library (e.g. from "tfl47024.pdf" --> "Smith 2009 - Psychological aspects of online communities"), which makes searching for pdfs a lot easier.

(2) It has a pdf reader integrated into the program, so that you can see the text as you are browsing through your library.

(3) Like EndNote, It has an integrated search function that is directly connected to several search engines, including PubMed.

All this means that the next time you are looking for an article, all you need to do is open Papers to search for it, download it into your library, capture bibliographic information, and read it. Much as I love zotero, it can't do all those things. But I still use zotero, because I find that it is better at capturing bibliographic info, and its great for cataloging things that aren't pdfs (which is pretty much what Papers is limited to). Its too bad that they don't play well together (yet).

Of, and by the way, if you're going to be using multiple computers, you can put your zotero home directory into Dropbox, which allows you to have access to your bibliographic data from any computer with a browser.
posted by googly at 9:26 AM on June 5, 2009

i'm following this question, too, and interested in opinions for non-mac users!
posted by yonation at 11:26 AM on June 5, 2009

Also consider Mendeley, or for a system with less overhead, CiteULike
posted by chrisamiller at 11:33 AM on June 5, 2009

Love Zotero, and I think Googly's Dropbox solution is no longer necessary, since the new Zotero syncs automatically to their servers, so you can have the same collection on multiple machines.
posted by Mngo at 12:14 PM on June 5, 2009

The current Zotero version will also (batched) take a pdf file, fetch metadata, and name it appropriately. You have to install the pdf2text separately, but it's straightforward and will keep the full-text index in Zotero for you to search on.

I take advantage of the html-snapshots which you can get from many journals to include my highlighting and notes within Zotero. I like using the (private) groups feature to keep shared libraries with my lab; we are much more efficient at keeping track of a topic collectively. It's nice to add tags and notes to items in addition to the auto-tags.

for BibTex, Zotero will export to that format. If I'm writing a paper (or a proposal, or anything long) I create a folder or tag for that paper, and copy every item that I decide to cite there or tag it with an id like ResequencingGrantProposal. I can then right-click and export the collection as BibTex. Every item is auto-generated a bibTex name, almost all of which work out sane and easy to use. Ctr-alt-c gets you the whole bibtex entry (including name) to paste; they plan to add soon a quick-copy of just the bibtex name.

Unfortunately, you either have to keep a running version of the bibtex file with the quick-copy output (which I do, to get the name) or re-export everytime that you want to rebuild the latex file.
posted by a robot made out of meat at 6:18 PM on June 5, 2009

Collections and tags have a lot in common in Zotero. They are basically identical except collections can be arranged hierarchically; whereas tags can be easily 'AND' filtered using the nifty tag browser and tag names are indexed for quick searches.

My advice is, choose carefully and deliberately in advance between using collections and tags, because it's not easy to change later.

I chose to use tags for basically everything. I only used collections for "task" related categories like "Just imported from file 5 June 2009" and "Things to send to Antony".

(Funnily this is basically the opposite of what Zotero developers seem to have had in mind. I tried to encourage them to essentially merge the two concepts or at least make them as good as each other, but it didn't end up happening. Every now and then someone begs for hierarchical tags though. More.)

For bibtex, I advocate exporting your entire library to bibtex. Why not? It only takes seconds for 100s of items. They haven't yet implemented a feature to automatically sync to a bibtex file.
posted by hAndrew at 12:27 AM on June 6, 2009

Papers is great, but it's exactly what it only works with what it says: papers. It was designed by people working in the life sciences, where pretty much all academic traffic is in papers. In my work, though, I end up needing to work with books, web content, and other media content and Zotero supports that much more fluidly. So it depends on your field - maybe this restriction will matter to you, maybe not.

I'm not sure what Papers' citation system is like (does it even have one? I can't remember), but Zoteros is decent. It didn't work with the latest version of Word last time I checked, but that was definitely on the road-map.

As for organization, I think it's really up to your style. I'm not very deliberate about my organization, but I haven't hit my head against any particular walls so far.
posted by heresiarch at 2:49 PM on June 15, 2009

To clarify: I think Papers is substantially better than Zotero for managing actual files. If all you want to work with is PDFs, it's wonderful. But since I had non-PDF content, having to maintain multiple libraries was too annoying, and so I use Zotero instead. If you can use Papers, I think you should look very closely at it.
posted by heresiarch at 3:00 PM on June 15, 2009

Response by poster: So I just joined my lab last week, and it turns out that the PI is using Sente, for which we have several extra licenses. Is anyone familiar with Sente? Anybody know about merging Zotero and Sente?

Thanks.
posted by solipsophistocracy at 10:57 AM on July 16, 2009