Tech and geospatial

This digitised life … (with Zotero)

There are quite a few open source applications around that are at the point of being sufficiently well developed to be of practical use for a professional on a day to day basis. Those that immediately come to mind include Open Office, Inkscape, the GIMP, the strangely named ‘gvSIG‘ (GIS) and of course the bibliographic application Zotero that I discuss in this post. That’s not to say any of these apps are not useful, reliable or popular but rather, that very minor issues sometimes mean that their day to day use is not entirely problem free in some scenarios. It’s not a universal scenario, but is certainly something I have noticed.

Interesting Things In My Library #7
Interesting things in my library #7 (Flickr User AussieRupe - Rupert Scammell)

Zotero impressed the heck out of me when I first began using it regularly. Early versions were a little buggy, occasionally crashed,  had limited support for in-text citations and also caused random database craziness. Indeed, until the beta of V2.0, I could only use Zotero as a tool for quickly adding new items that I had found on the web to my master bibliography, held in Endnote. But that rather unique functionality was enough to make it a permanent resident on my mac. It was good, and certainly very promising, but just not good enough to use (or trust) with my entire bibliographic database. So I used it and abused it, leaving it running in the bottom of my browser window where it would store small batches of new discoveries for a few days at most before they were exported to Endnote.

Fast forward a year or two and as most people would be aware the Zotero developers now have a very stable and extremely useful 2.03 release behind them: the app – a gem of an idea – has evolved into a beast. There are so many  advantages to using Zotero for managing my research sources that I really don’t know what I would do without it now, and many of these benefits are fairly well covered on the Zotero website. However, Zotero is not yet my one stop reference manager for a few small reasons and, with the view that constructive criticism can be helpful, I thought I should outline those here.

Support for in text citations (or rather a lack of support) has long been an issue. There are now citation plugins for both Mac/Win Microsoft Word and Open Office (as well as OO on Linux), however I still find them a little frustrating to use. They lack contextual menus and while the commands work fine most of the time,  very occasionally the plugins fail completely and require a reinstall. These are certainly not major issues, more inconveniences. But as I suggest below, mere inconveniences become much more than that in a professional workflow with very hard deadlines, real clients and where one doesn’t tend to have time to mess about fixing things.

Editing citation/bibliographic styles with Zotero is not for the faint hearted. Indeed, it’s quite difficult and requires a degree of computer literacy that I and many others don’t have. While there is an active community who have developed a good range of styles that you can download it’s not possible for mere humans to edit these styles. Why would you want to edit an output style? Put simply, to ensure that your reference list meets the requirements of publications whose styles are not currently supported. Endnote handles this same problem well: one simply copies the nearest similar style, makes some minor changes using their style manager and you are done. Zotero has a long way to go in this regard.

Searching is important to me, indeed, it’s critical however Zotero has somewhat lacklustre search abilities. I have a very large database, not only of sources but also accompanying notes and PDFs, different kinds of sources for different projects and so on. While doing a quick search for a term or author is easy, advanced search options are basically absent. I suspect that the ‘smart folders’ tool is there to provide some of the advanced search capabilities I need, but I haven’t yet been able to add more than one search criteria to a saved search which limits its effectiveness for me. Perhaps there’s something I’m missing? Better search gives users more control.

The Firefox browser is not where I like to work. While Zotero has decent integration with my desktop environment – including dragging reference lists into other apps or drag/dropping of PDFs into the Zotero database itself – I still find it a source of ongoing frustration to work inside a browser. Fortunately, they are working on a standalone desktop client. Bring it on: Zotero is the only reason I continue to use Firefox at all.

Zotero is very important to me; it is a potentially very powerful research tool that any serious researcher should be using in some way.  Proxy support, syncing/sharing to the web, wide support for importing new sources and many other attributes make it a research-centric tool not matched elsewhere. Frankly, the inability to edit styles in Zotero is the only issue that prevents me from fully (and permanently) incorporating this wonderful application into my professional workflow. In a document with 10 or 20 citations, this limitation is really only a mere inconvenience however if you regularly work on projects with 10s or 100s of citations – as I do – then it’s a deal breaker. I’m not going to edit large reference lists manually.

So, overall I think that the app is almost there; indeed, I really really want it to get there soon. It has become the central store for all reference materials across all of my projects, which means I trust it with the results of years of my hard work to accumulate a useful reference database. It’s stable and dependable and despite day to day use for quite some months now I have not had a single crash or error since I installed the 2.0 beta. The issues I highlight here then are very minor complaints indeed and are far outweighed by the advantages of using this app. If you are yet to try Zotero for yourself, I can not recommend it enough. To the Zotero developers: thankyou – this humble researcher is eternally grateful!

Edit 3 June 2010: Reader Sebastian, in a comment below, has pointed out this discussion on the Zotero forums about editing styles and a project underway  linked to Mendeley called ‘csledit‘ that will, hopefully, resolve the style editing limitation. Good news indeed. Thanks!

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4 replies on “This digitised life … (with Zotero)”

Michael, I enjoyed reading your post and wanted to offer a few suggestions for some of your issues. First, you can chain as many advanced search criteria together as you like by clicking on the plus icon next to the criteria. You can see that in action in this video.

You are right about some of the difficulties associated with the Citation Style Language. There are plans to develop a more user friendly editor. However, there are currently a great group of open source developers committed to the project who are happy to help grow the style repository. If there are a few specific styles you would like consider requesting the styles in the Zotero forums.

Best, Trevor from Zotero

Thanks for your comments, Trevor.

I probably didn’t explain the search issue very well- I can see it has been designed for chaining criteria together however for some reason it resets my attempts at doing this so that only one criteria is ever saved. Not all the time, but enough to cause headaches.
Re styles: I have held off on requesting new styles for now, partly because the changes I often need to make are very minor ones and for small circulation journals, so I expect that it might not be worth the effort for a dev to look at. Still, it’s good to know that option is there though I certainly look forward to a CSL editor!

about styles –
Mendeley, which uses the same style format as Zotero, is developing a free (and open source afaik) style creator which should be ready for use soon.
The principal reason this hasn’t happened earlier is that csl – the Zotero format – is a lot more powerful than Endnote’s .ens – it allows for better and more stable styles. So Endnote isn’t really doing this better in any meaningful way.
See the discussion here

Thanks for that link Sebastian, it provides some good context and so I’ve added it to the bottom of my post. Evidently the citation styles issue is reasonably common problem. I am sure that, once complete, the new CSL editor (CSLedit?) will be more functional and useful than the Endnote style editor. I look forward to it!

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