Zotero - reference management software review

I've been writing my thesis - but not writing it "up" - for a couple of months, and although I've previously managed all my references manually, I decided that I'd use some reference management software as I wrote my PhD thesis.

I've previously been happy to write all my references the old fashioned way - by looking at the book / journal, and writing down the salient information in the bibliography, and writing out my in-text citations manually. This method has always served me well and because I am a pedant when it comes to things like spelling, grammar, punctuation and indeed referencing, I have been able to manage my references flawlessly in this way. I haven't made mistakes because I know how to reference (Harvard-style) and so I continued with the mindset of "if it ain't broke, don't fix it".

However, since the number of references I'll probably be using for my PhD thesis was likely to be far greater than those I used for my essays and MA thesis, I decided that I'd start using some reference management software to help me keep track of it all. I'm glad I've taken the plunge, because even at this early stage, I already have 74 items in my reference list! (I've not fully read all of them yet though.)

So I decided that before I got started on my thesis, I'd compare / try a few reference management software (RMS) programs and decide on one which I was happy with. I probably spent nearly 2 days faffing around with RMS and making up my mind, but I was hopeful then - and I'm convinced now - that that was time well spent.

The RMS I settled on was Zotero. Below I list some of the other main RMS and why I chose not to use them:

• Refworks - this was the one which I had heard of most, and so was the one I was originally intending to use. Then I learned that unless your university had a subscription to it, individual students had to pay to use it (and that the University of Nottingham does not have a subscription to it). This quickly put me off Refworks.

• Endnote - The University of Nottingham does have a subscription to Endnote, so this became top of my list. I tried to follow the instructions I found for how to set up an account, and the instructions were unfathomable (for starters, they referred to a different version of Windows than the one on the library PC I was using, so were impossible to follow). I tried to get some help from an online chat person/bot, and from the IT support people in the library, but they struggled to use it too. This is not a criticism of them, but a criticism of Endnote, as I usually find them to be really knowledgeable and helpful. At length, with the help of an IT support person, a YouTube video, and an online help sheet, we finally managed to get the program running. I thought it'd be plain sailing after that, but it wasn't. The way to get an article onto Endnote seemed to involve a very complex procedure of searching an online library database... well, some of the sources I'd already taken a look at aren't on an online library database, and working out how to get these sources onto Endnote seemed impossible to me. Added to which, the 'main' version of Endnote could only be accessed from university PCs, and I'm likely to be doing most of my work from home. So I gave up on Endnote.

Once I'd dismissed these two 'big names', it was a question of doing some comparisons of the alternatives. I looked at a few online comparisons, and screenshots of different RMS systems, and downloaded a couple to try. I can't remember which ones (so this part of the blog post isn't that enlightening, as I can't recall why I dismissed Mendeley, BibTex and whatever else. What I can do is explain why I chose Zotero and why I like it).

Zotero - just click the Download button and Bob's your uncle.

Reasons why I like / chose Zotero

1. It's easy to use. This reason is up there front and centre of the reasons I chose Zotero. Here's how you do it: (1) go to Zotero website. (2) Download Zotero software that takes about 1 minute. (3) Start using it straight away. The Word plugin only has 5 buttons on it (add/edit citation, add/edit bibliography, refresh, unlink citations, and settings). It did take a little playing around with to work out all the functions, but more on that later.
2. Metadata is automatically uploaded to Zotero. Until I looked into RMS, I didn't even know what metadata was (data about data, I would have assumed). Metadata is in fact the details of a document such as its title, authors, publisher, date, URL, DOI, and suchlike. Having tried a few RM systems, it became evident to me that the sheer amount of time it can take to add metadata is just ridiculous on some applications. It can take a minute or two - at least - to write out all the metadata for one file. When that's multiplied by the possibly 300+ sources I may use during the course of my PhD, I realised that that would be a lot of time wasted and a lot of tedium suffered. The fact that Zotero automatically detects and uploads all the metadata on almost every file you drag and drop onto it was a godsend to me: "future me will thank me for this" I thought, and indeed I am grateful to past-me for choosing software which automatically sorts the metadata. And when metadata isn't detected (which has only happened on one online source so far) it's easy enough to enter it yourself with Zotero.
3. Zotero allows me to upload PDFs and other files whilst keeping those files on my computer. This is a must for me, because tech isn't always as trustworthy as we'd like it to be (yeah, I know my PhD thesis is about why we should trust tech to care for the elderly, but this is an entirely different issue!) If a company suddenly goes offline, into liquidation, etc, then I'd like to be able to have all - or at least, many - of my files stored offline on my hard drive as possible. Zotero ticks this box whereas so many other RM systems don't. This also appeals to me because I like to edit my PDFs with notes and symbols and things which aren't available in some RMS dedicated editors. eg some of the other RMS will allow you to edit a PDF, but only within the RMS program; if you then try to view that PDF in Adobe or similar, you can't see any of your notes. Or, the software allows you to highlight but not annotate PDFs on the page itself. Zotero allows me to edit documents with Adobe, Nitro or any other program, and then upload them as they are.
4. The code for Zotero is open-source. I'm not a software buff but apparently this means something along the lines of: if Zotero goes out of business, another company could use the same code to make the same program and so I'd still be able to use it. Or something like that.
5. Zotero is cloud-based, so wherever I am, I can access my saved sources, and the files can be viewed and accessed even if the source file is not on that computer. For example, say I annotate a PDF which is held on my home computer, and then I drag and drop it onto Zotero. The file is still on my home computer, but now if I go into uni and use a PC in the library, I can access and edit the very same PDF (with my notes already one it) even though it is not saved on that uni PC. This is a great feature which I didn't even realise was a feature when I started using it, but I find it really good. Most RMS is cloud-based, but still...
6. There's a Chrome plugin which allows you to upload sources direct from the web. The plugin takes about 30 seconds to download and sits right next to the URL bar. The program detects what type of page is being viewed (eg a news article, journal article, blog etc - I guess that's the metadata doing its job again!) and so when you click the icon, it knows what metadata is needed (date of publication, issue number, etc.) Amazing!
7. Sources of various different types can be uploaded. PDFs are standard for RMS, obviously, but some of the other RM programs I came across couldn't seem to handle a news website, let alone a Word document, powerpoint presentation, TV programme or a jpeg image. Zotero can handle any and all of these - and lots of others too.
8. I can use it as a cloud-based way of saving my own work. Because Zotero can handle Word documents, I made a folder within Zotero called 'my work' and now I upload my work to it at the end of each day as an additional cloud-based backup in case my house burns to the ground during the night. I suppose this wasn't the intention of Zotero, but it's a nice feature I'm utilising for my own gain.
9. It's easy to write notes and summaries. There's a text box on the right-hand side which you can write whatever you like into. I'm using it to write notes and summaries of documents. I know this is standard in almost all RMS, but it's obviously a useful feature!
10. It's possible to tag sources and link sources to one another. This is probably a simple feature which may be available in other RMS, but it's useful nonetheless. For example, I have scanned and uploaded a few different chapters of the same book, and although each chapter is written by a different author, I wanted them to be linked to one another, so that was easily done. I've also tagged my sources with various content-related tags like 'consent' and 'harm', but also 'fully read' and 'not yet read' to help me keep track of what I have and have not read. As one would expect, you can search for particular tags.

Screenshot of some of my Zotero sources at the moment

One wish

I saw on one RMS - I forget which now - that whenever you highlighted some text within a document, it transferred the quote to some sort of clipboard / note-taker interface. This seems like a really useful feature which it would be quite nice if Zotero had, but it doesn't. I suppose that's because it is a file depository rather than a file editor. My highlighting has been done in Adobe/Nitro, and not through Zotero itself; Zotero essentially just keeps a copy of the file. It's not too great a problem though, because it's still easy to cut and paste quotes if I want them.

Using Zotero

For the most part, Zotero is pretty easy to use. you drag and drop the files you want into the window as shown above. You download the Word plugin, and when you want to add a citation, you just click 'Add citation', type in the author or title you want to cite, add the page number, and press Enter. Pretty simple. And indeed far simpler than the other RM systems I had a go at.

But of course, there are always some times when there are slightly trickier things that one wants to do, like adding metadata, having one source with multiple sources attached to it, and it wasn't particularly easy to find Zotero help / guides on how to do these twiddly bits. I did find one help guide from Zotero, but this isn't exhaustive. I worked it out for myself though and wrote it down - here is my help sheet. Anyway, I've found Zotero to be pretty intuitive and easy to use, and I'm glad I took the time to choose a RMS programme which suited me and what I wanted. I definitely have no complaints so far.

Black Friday: No thanks - just bargains

It's that time of year again - Black Friday. The time of year when people clamour for bargains, enthusiastically elbowing others out of the way in a frenzy of desperation to save a few quid buying consumer goods at knock-down prices. That time of year when, for a week or more, people are glued to their smart devices (even more so than usual), in the crucial search for stuff.

Apparently, Black Friday has been with us in England for eight years now. It's long been an American trend; it's the Friday after Thanksgiving. But whilst Brits - and probably numerous other countries - have been only too happy to adopt the greedy fight for cheap electronics that encapsulates Black Friday, we seem to have no interest at all in the ethos which precedes it in America. We don't want to give thanks; we just want bargains.

I know that Thanksgiving has its history in colonialism, pilgrims, and has a religious spin to it, but even though I'm an atheist and a Brit, I think there is something worthwhile in the festival which we would do well to adopt. A general disposition of gratefulness is something that is probably quite good for one's mental health. Life is busy and it's no wonder that there's been a growth in mindfulness and relaxing activities like adult colouring books, meditation, yoga etc. Reminding ourselves of everything we are grateful for is a worthwhile exercise in itself, even if we don't say it out loud around a table full of turkey and pumpkin pie the way Americans do. I know I'm grateful for good health, my wonderful son who brings joy and meaning to my life, and for my family and friends. I'm grateful that I've recently started a relationship after nearly 7 years of being single. And I'm grateful that I have the opportunity to study for a PhD and that I'm being funded to do so.

All of this gratitude - the very essence of Thanksgiving - seems intrinsically valuable, and it's a real shame we don't adopt this festival. But what's more sad is that we're only too happy to adopt Black Friday, the fight for cut price electronics, clothing and suchlike, whereby we're implicitly reinforcing in ourselves the idea that garnering more stuff will make us happier.

Perhaps I'm being too cynical: perhaps everyone uses Black Friday (which has somehow morphed into a week or more of sales) to purchase gifts for their loved ones in time for Christmas. And they use these gifts to spread the love and bring about gratefulness, wellbeing and happiness in those around them. Yes, that probably happens to some extent. But I just don't think that these HD TV's and Playstations and iPhones are all being given as gifts. And maybe it's none of my business - if people want to buy an iPhone cheaply for themselves then why shouldn't they? Well, yes, my revulsion at the fight for bargains is not iron-clad proof that Black Friday is somehow morally wrong.

I just wish that we would adopt the disposition of gratefulness for what we already have, and appreciate that the people around us are what really makes life worth living.

Thesis-writing book reviews

I've now read these four books about thesis-writing for PhD study, and I share my thoughts on each of them below.

• Murray (2017) How to write a thesis (4th ed). Open UP Study Skills. Open University Press
• Carter, Kelly, and Brailsford (2012) Structuring your research thesis. Palgrave Research Skills. Palgrave Macmillan
• Oliver (2008) Writing your thesis (2nd ed). Sage Study Skills. Sage Publications
• Williams, Bethell, Lawton, Parfitt, Richardson, and Rowe (2010) Planning your PhD. Pocket Study Skills. Palgrave Macmillan

I've also bought "How to survive your viva" by Murray, but I haven't yet read it; I'll review it at a later date perhaps.

Murray (2017) How to write a thesis

This is a great book - the best of the four - and well worth the £20 I paid for it. I don't often write or highlight in books, but with this one I did because there are some parts of it which are stand-out gems of advice that I wanted to be able to find again and again.

I'd say that this book would be of particular use to people who might find it difficult to get started writing (or continue writing) or people who believe that they have nothing to write about (yet), because the book is filled with writing prompts, ways to get started, ways of planning, and ways of structuring your work. It's written for a generalist audience, but the suggested exercises seem flexible enough that there can be something useful for everyone, whether they are writing about biochemistry, medieval literature, or international politics. With 311 pages, it is bursting with useful tips, advice and information for thesis-writers.

I'm not someone who finds it difficult to get started writing, but I've still found the book really useful - and full of encouragement too! Almost every page has something really useful on it, and I can't praise this book enough. Here's a quote:

"In writing a thesis, we are entering a debate; there are many people who will not agree with our writing. Not only can we not ignore the work of those who are likely to disagree with us, but we must directly address it. We have to articulate the basis of such disagreements in our writing, showing where our work fits into the debate." (p121)

There are sections on getting started, structuring, becoming a 'serial writer', editing and revising work, and some information about the Viva. The only 'criticism' I have of the book is the suggestion that we should try to write 1,000 words a day. You don't need to be doing your PhD in maths to realise that 1,000 words a day for 3 years is over a million words! I suppose many people may struggle to write and so the chance of this actually happening to them is minimal: for me, over-writing is a genuine danger. Typically my way of producing the 4,000-word essays for my MA studies was to write an essay of around 15,000 words, then to cut it down and distill it. The thought of distilling 1,000,000 words into 70,000 words is unappealing, and so I'll take Murray's advice with a pinch of salt.

Nonetheless this book is fantastic, and something I'm sure I'll return to again and again throughout the next three years.

Carter, Kelly and Brailsford (2012) Structuring your research thesis

I found this book a bit weird. It is supposedly written for a generalist audience, as one would expect, but in some parts of it the advice seems very specific to particular domains. There is also a lot of what I can only describe as 'waffle' - which would be fine if it were a lengthy book which can afford to go off-piste from time to time, but with only 84 pages I would say it should stick rigidly to the point, which it doesn't seem to manage.

Something else which bothered me is the style in which it is written. I know it is aimed at an educated audience, but nonetheless, the goal of a textbook - any textbook - should be to explain what needs to be explained in the most efficient way possible; a textbook is not (or should not be) a chance for the authors to show off their articulacy with flowery language unless it is really necessary to the cause. This doesn't necessarily mean dumbing down, but it does mean using concise language where possible. Some sections of this book were unnecessarily verbose - here's a quote which is supposedly about how to make a common thread run through your thesis:

"Because it makes use of the complex semiotics of poetic language, metaphor can also be a strong structuring device. Metaphors that have a cultural underpinning enable a researcher to inhabit a social or cultural space simultaneously with their academic one. Cultural metaphors demonstrate the way that metaphor can contribute to methodology, and our examples make explicit the deep-level functioning of metaphor to carry one set of connotative meaning into another field." (p8)

I am struggling to know what the take-home advice of this paragraph is, and this quote is by no means an isolated cherry-picked example of the way this book is written. Whilst there are some parts of the book which may be of use to a thesis writer, I found the general tone of the book strange and at times almost impenetrable. And so given its price and low page count, I would say that - unusually for the Palgrave study books - this is just not worth the money.

Oliver (2008) Writing your thesis

[NOTE - There's now a third edition of this book, but I have the second edition pictured here.]

This book is really useful, and is a really good accompaniment to Rowena Murray's book, because much (around half?) of the material in this book isn't covered in the Murray book. For example, logistical and technical advice about fonts, layout, use of Latin terms, referencing, academic conventions and suchlike. There's also a useful chapter on working with supervisors and examiners. 

I think that if you're a person who is motivated and ready to start writing, then this book is probably even better than the Murray textbook. But this book does assume a certain readiness to begin study, which not all people will feel. It's fairly concisely written  and provides a happy medium (174 pages) between the brevity of the Williams book (below) and the detail of the Murray book. Here's a nice quote about thesis introductions:

"This [the Introduction] is a very significant chapter in the thesis. As it is the first chapter which is read by the examiners, it inevitably creates an impression in their minds about the writing style of the student, and of the broad nature of the thesis. The main purpose of the introduction is to provide the reader with an overview of the research study, and of the key factors which were influential in its inception. It sets the scene for the reader, providing a glimpse of the setting for the research and of the methodology. It should also provide a statement of the aims of the thesis." (p84)

The down-side of this book (for me as a Philosophy student, at least) is that the chapters on the literature review and methodology were largely irrelevant for me. Notwithstanding these chapters, the book as a whole is a very useful one I'll no doubt return to several times throughout my doctoral study. 

Williams et al (2010) Planning your PhD

This book is only tiny - smaller than A6 - and only 120 pages, but it packs a lot in. Brevity and ease of use are its assets.

As the title suggests, its focus is on planning and preparing for a PhD, and it's probably of most use to those who have not yet written a PhD research proposal. Once you've written a proposal and had it accepted, most of this book becomes redundant (I should have bought it before I wrote the proposal to have got the most out of it!)

Nevertheless, there are a few pages (perhaps 15 - but remember that each page only has around 300 words on it!) about introductions, literature reviews, attending conferences and publishing in journals, which are brief but of use. This book by itself would be insufficient to use as a guide to writing a PhD thesis, but given that its intention is to help you plan your PhD, it does exactly what it says on the (very small!) tin.