Organising Your Research: Advanced Zotero

Now where did I read that quote? What did that book say again? Was the argu­ment in this chap­ter coher­ent?

For any­one work­ing in a research field I’m will­ing to bet that you have asked your­selves such ques­tions, and it only gets worse the more you read. So after the post on Reading last Friday comes this time­ly post on how to organ­ise what you have read. As with most items in our toolk­it there are sev­er­al dif­fer­ent options for work­ing at this stage of the process, how­ev­er I’m only going to con­sid­er one today: Zotero. This is main­ly because Zotero works at engag­ing with mul­ti­ple dif­fer­ent tasks in the research process. At one lev­el it is a full fledged ref­er­ence and cita­tion man­ag­er, while at anoth­er it is a syn­op­sis and sum­ma­ry data­base, and at yet anoth­er it is a library and data­base organ­i­sa­tion tool. I feel that Zotero com­bines the best aspects of sev­er­al oth­er tools, and does it with­out a lot of the bugs or cost of some of the big­ger names (cough Endnote comes to mind). Personally I use Zotero as a bit of a hub with­in my research process, arti­cles and infor­ma­tion get fun­nelled in and then spokes radi­ate out towards dif­fer­ent tasks and then infor­ma­tion is returned for fur­ther col­la­tion and use. This post is how I use Zotero.

The Basics

Simply speak­ing the basics of Zotero work as fol­lows:

  • Import or add ref­er­ence into Zotero from the var­i­ous plu­g­ins and data sources (Amazon, Ebsco, PubMed, Libraries etc) or input by hand.
  • Cite ref­er­ence in your text
  • Sit back and mar­vel at not hav­ing to man­u­al­ly for­mat ref­er­ences.
My Zotero Library

My Zotero Library

At the first lev­el, that of mak­ing your work of ref­er­enc­ing eas­i­er, Zotero does an admirable job. It is quick, easy to get data into, doesn’t crash reg­u­lar­ly (Endnote should take notes), syncs over the web, and out­puts in a wide vari­ety of for­mats with lit­tle fuss. Even if this is all you use it for, it is a great time saver and helps with tam­ing your cita­tions from  brusque unruli­ness to a gen­er­al surly atti­tude. However, Zotero is capa­ble of so much more than this, and to leave the process here would be to ham­string the use of the tool. But first a brief caveat.

Caveat: Zotero is exact­ly like every sin­gle oth­er com­put­er appli­ca­tion, in that it is a bunch of mechan­i­cal­ly exe­cut­ed code. 1 It can­not think for itself, and while it has a whole bunch of smarts built in, it can only deal with the data that you feed it. So in true com­put­er ter­mi­nol­o­gy it is sus­cep­ti­ble to the fail­ings of Garbage In, Garbage Out. Simply put if you feed Zotero, or any oth­er pro­gram, garbage data, then expect garbage in return; it can only work with what you feed it. So if your cita­tions have the wrong pub­lish­er, or incor­rect­ly entered titles (yes cap­i­tal­i­sa­tion here counts), then you will get that out in return. This is the most com­mon mis­take I see with Zotero usage. I cant empha­sise it enough, police and parse your data on the way in so you get well for­mat­ted and unruly data on the out­put. It is also worth not­ing that most library sys­tems, includ­ing Library of Congress, and pub­lish­er data won’t con­form exact­ly to your require­ments. So things like the pub­lish­er ‘WB Eerdmans Inc.’ will need to be man­u­al­ly stripped back to ‘Eerdmans.’ This is extra effort, and is actu­al­ly why I rec­om­mend that stu­dents only writ­ing short­er essays (com­mon­ly ~2000 words) sim­ply write and for­mat their cita­tions man­u­al­ly.

Research & Organisation

messy-office-03That caveat aside, and arguably because of that caveat, we will con­tin­ue on to the big­ger and greater things that Zotero is capa­ble of. If you are any­thing like me, you will prob­a­bly dis­like hav­ing a desk full of pieces of paper and var­i­ous jour­nal arti­cles that have been read, or still yet to be read, or have been read but not sum­marised etc. For about 10 years of my pri­or research life this was my over­whelm­ing bug­bear. I would reg­u­lar­ly lug a ream of paper around with var­i­ous jour­nals arti­cles print­ed out, and swathes of pos­tit tabs through­out them. These days I deal pri­mar­i­ly in PDF, and dig­i­tal high­light­ing and anno­ta­tion make this process much eas­i­er. But how do you organ­ise this infor­ma­tion? All those a3532582920.pdf and pubmed_83928932.pdf, not to men­tion the assort­ed .epub files of Open Access books, and much more. Well this is the sec­ond phase of how to use Zotero, and where it comes into its own.

RenameFileThe first fea­ture is some­what mun­dane: renam­ing. Once you have a ref­er­ence in Zotero you can attach or link a PDF to the ref­er­ence and sim­ply rename the file from the meta­da­ta in Zotero. It’s a sim­ple fea­ture, but saves a bunch of time and effort.

tagsSecondly, and more crit­i­cal­ly, as a dig­i­tal ref­er­ence man­ag­er you can add all your ref­er­ences to Zotero, and then sort and organ­ise them by two dif­fer­ent meth­ods. Firstly, you can sort them into cat­e­gories. I pre­dom­i­nant­ly use col­lec­tions for the­mat­ic organ­i­sa­tion, as you can see in my screen­shot: ‘Christology’, ‘Luke.’ Furthermore these col­lec­tions can be nest­ed, as in my ‘Psych’ col­lec­tion with var­i­ous sub-col­lec­tions under­neath. The sec­ond way to organ­ise your library is through the use of tags. I tend to use tags in three dif­fer­ent fash­ions: top­i­cal, pro­ce­dur­al, and project ori­ent­ed. Topical tags sim­ply delin­eate the var­i­ous top­ics that are addressed by an arti­cle or book. Procedural tags gen­er­al­ly mark whether some­thing is yet to be read (toRead), or yet to be marked up (toMarkup). Project tags sim­ply note that I used a cer­tain arti­cle in a project I have worked on. The entire Zotero data­base is search­able by these tags so you can eas­i­ly and quick­ly have an idea of what is yet to be read or marked up, or what you cit­ed for a cer­tain paper, or what deals with cer­tain top­ics. Super sim­ple stuff, but invalu­able in being able to find mate­r­i­al quick­ly when your library grows large.

Documentation & Gathering

zoteronotesThe penul­ti­mate phase of the Zotero expe­ri­ence comes in being able to col­late and find your doc­u­men­ta­tion and notes on all the books and arti­cles. Within Zotero you can add ‘Notes’ for each ref­er­ence. I use these notes in two ways. Firstly if I’m work­ing with a dig­i­tal resource tend to have a sin­gle note ded­i­cat­ed to all the high­lights from that resource. You can extract these sim­ply, and I’ll cov­er that in com­ing weeks. If it is a phys­i­cal resource then I tend to tran­scribe either the full quote of inter­est, or briefly sum­marise the idea at hand, and note page num­ber. That way the key pieces of infor­ma­tion are eas­i­ly at hand. This is the markup phase of my ’toMarkup’ tags above. Secondly, I also write a brief 50–100 word syn­op­sis of each chap­ter or major log­i­cal sec­tion of the ref­er­ence, in my own words. This allows for bet­ter mem­o­ry reten­tion of the mate­r­i­al, but also pro­vides a good ref­er­ence syn­op­sis of the work and there­fore makes it eas­i­er to engage with at a lat­er date. These Notes are stored along­side the ref­er­ence and are synced across devices, and so are eas­i­ly acces­si­ble any­where. Furthermore, they are emi­nent­ly search­able and while my office used to look like it was over­flow­ing with a small dead for­est, and pre­vi­ous­ly I would be scram­bling around in var­i­ous mani­la fold­ers and a whirl­wind of post-it notes to try and find the source of a quote, I can now search for it in Zotero, and in pret­ty short order I have found the doc­u­ment I am after. This is one of the fea­tures of Zotero that I find invalu­able these days.


The final phase of my Zotero work­flow is to actu­al­ly out­put the ref­er­ences as cita­tions in my doc­u­ments. While Zotero does come with Word, LibreOffice and OpenOffice plu­g­ins, I find all of those word proces­sors annoy­ing and ulti­mate­ly unsat­is­fy­ing. I pre­fer to use Scrivener, which I will talk about in due course. But unfor­tu­nate­ly Zotero doesn’t come with a default Scrivener plu­g­in, although I’m hop­ing for one even­tu­al­ly. Rather you can use the RTF Scan fea­ture of Zotero, which makes it use­able with any­thing that can out­put in RTF for­mat. In order to ref­er­ence mate­r­i­al you sim­ply use the short code, con­sist­ing of {Author, Date, Page} or any one of the oth­er short codes depend­ing on your usage. You then run your out­put through Zotero and choose your stylesheet and bam, all your cita­tions are done. It doesn’t get much sim­pler than that.

The final note goes to the stylesheet func­tion­al­i­ty. There are many ref­er­enc­ing for­mats out there, and Zotero is invalu­able when you need to refor­mat an arti­cle or paper for a dif­fer­ent ref­er­enc­ing sys­tem. All you have to do is down­load the new stylesheet and apply it to the doc­u­ment. There is a whole data­base of Zotero stylesheet (CSL) files out there for var­i­ous for­mat­ting sys­tems, and the major­i­ty you can find here:

If you are an SBL 2.0 user, you will find that the style on the repos­i­to­ry is one that uses Ibid. nota­tion. Given that the no-Ibid option seems to keep dis­ap­pear­ing, here it is for pos­ter­i­ty. soci­ety-of-bib­li­cal-lit­er­a­ture-2nd-edi­tion-full-notes-no-ibid


That just about wraps up this post on Zotero, as I said I find it the cen­tral hub of my research method­ol­o­gy. Although I’m sure that there are oth­er tools out there. Perhaps Endnote has become the phoenix from the ash­es and res­ur­rect­ed itself with­out crash­ing every 15 min­utes, or per­haps you pre­fer a dif­fer­ent tool. As usu­al I would love to hear your com­ments and what you use in the sec­tion below.


About Chris


  1. ok some genet­ic algo­rithms exclud­ed