Bibliographic Reference Manager Wars

It seems to me that competition is heating up between the different reference managers that are available. I am seeing more people using Zotero and Mendeley, although Endnote is still the weapon of choice for most people. However, the other two products are free, at least if you do not need the extra storage space available for a price.

To consider Mendeley first, I confess that I have never got on with it very well. The interface into Word has been cleaned up significantly and it does work, but except for Science Direct I have not been very successful in capturing online papers and other references, for example from JSTOR. Perhaps it is just me.

The other thing which people do object to with Mendeley is that, in April 2013, it was brought by Elsevier, the publishers. Firstly, the question that springs to mind is “why?” According to this article, it is to gain access to the data flows of all the article sharing and groups and so on that the social media side of the product produces. That, of course, is modern business for you, but you might object to your data being used in this way.

The downside of the sharing ability is, of course, the potential breach in copyright. Indeed, the article referred to above notes that Elsevier were one of the protagonists in trying to stop PDF sharing, so that every researcher had to buy their own copy from the publisher. The pros and cons of this are, of course, arguable, but breaching copyright is actually illegal.

Next up is Zotero, which has improved radically over the last few years (i.e. since I last looked). The desktop version works nicely and (once I found the tools) the integration into Word seems fine (the tools are on the Word ‘Add-ins’ menu, but not named as Zotero, at least on my installation. Again, Zotero offers some social networking ability, although I confess I have not explored it as yet.

Finally, we come to the stalwart package of the field, Endnote. This is costly (at least in comparison to the others) and proprietary, although this does not mean that you are committed to using Endnote for evermore, as some people seem to think. All of these packages are interoperable, to a greater or lesser extent, although, annoyingly, some struggle to transfer attached PDFs (I’m still looking into it). Endnote is probably the most powerful, in that if the exact reference style you need is not available, you can modify one, which is not, so far as I can tell, available in either Zotero or Mendeley, at least without a great deal of blood, sweat, and XML.

Of course, with power and flexibility comes complexity, and Endnote is probably the most difficult of the packages to come to terms with. It also has an online version, which is developing rapidly (and rather confusingly) at present, but does not have social networking ability (at least, as yet).

So, there you, you pays your money (or not) and you takes your choice. As I mentioned, Mendeley would not do the things I wanted it to, and so I can’t recommend it. Zotero and Endnote seem to be converging to similar sorts of solutions, so far as I can tell.

Anyway, don’t take my work for it. A useful comparison can be found here: http://blogs.lse.ac.uk/impactofsocialsciences/2012/11/23/harries-referencing-tools/

Endnote vs The Rest

There is an interesting post here about using Endnote (or not):

http://thesiswhisperer.com/2013/08/21/endnote-vs-well-everything-else/

together with a lengthy discussion in the comments.

Endnote seems to have a bad reputation for occasionally messing up long documents, leaving a 'references-off-by-one' error, which is referred to int he post and comments.

I have not ever seen this error, so could anyone who does experience it let me know, please? Anecdotal evidence suggests that it happens when a long document scan for citations is cancelled, but I have not managed to reproduce it.

Aside from that, one of the outcomes of the discussion is that choice of reference management software is highly personal.

And finally, I have to add that lots of people do complete their theses happily while using Endnote....

Invalid Class String – Update

One of the most popular posts on this blog is the one about the error “Invalid Class String”.

This usually happens when you are running Word as an administrator and Endnote as a user.

Thompson have kindly rearranged their web site, so the link to the FAQ in the original post (http://durhamendnote.blogspot.co.uk/2012/05/invalid-class-string.html) is not incorrect.

The address you now need is this: http://endnote.com/support/faqs/endnote

and scroll down to CWYW 13, and click on ‘Answer’. 

Endnote X7.0.1 Windows

No sooner did Endnote X7 appear, than there was a patch.

The patch also uses a new feature of Endnote X7, in that it launches automatically when the update is detected, and installs itself.

The update arrived last week. You can skip it, but the pop-up may well return the next time you open Endnote. In order to avoid it keeping popping up, you need to click on ‘skip this version’. If you use ‘cancel’ it will reappear next time.

You also need administrator rights to install it, so it could become a nuisance for those without such rights (of course, that may be part of the point; updates are good things, in general).

The patch description is:

Improved stability for Synchronisation.

Updates to "Category Bibliography" functionality in CWYW.

Updates to record matching logic for CWYW.

Improved performance for application auto-updating.

Prefixes and Suffixes

Sometimes, the plain reference will just not do. Someone asked me recently about a work which was by a set of authors, but had a bit inserted in it by someone else. The plain reference (Smith et al (1991) p. 42) simply would not do, but then nor would (Jones (1991) p. 42), as that is almost equally misleading.

Similarly, you might was to say (see Smith et al (1991) p 55).

How do you handle these issues?

There are two ways you can, in fact, deal with these items. Inevitably, there is a complex way, and a simple way. Unless this sort of thing happens a lot to you, I commend the simple way.

Consider this citation:

(Cuban, 2001)

Suppose I wish to add the word ‘see’ to the beginning of it. If I click on Edit & Manage Citations from the Citations group of the Endnote tab, I get the dialog box:

I can add the text I wish to appear before the citation to the Prefix box:

(see Cuban, 2001)

I need to remember to add the space as well.

Endnote X7

For those of you eagerly awaiting the arrival of Endnote X7 I present the following video.

It isn't mine, but from a reliable source, and lasts just over six minutes.

http://www.youtube.com/watch?v=FqvYH0FUXps

Changing Temporary Citation Delimiters

I encountered an issue recently with Endnote which had been upgraded (from X4.0.0 to X4.0.2, but I’m not sure the exact details are important).

During the upgrade the temporary citation delimiters had been changed from “{“ to “(“.

A simple, slight change, you would think. What could possibly go wrong?

Well, Endnote, of course, started to throw a bit of a wobbly, putting up the Find Citation box for every parenthetical comment the author had made.

Fortunately, I discovered that this can be fixed in a relatively painless manner. Although I still recommend taking a backup before trying this at home.

You need to start with all the references in a formatted state. This might take some clicking on the Ignore button on the Find dialog when it appears.

Then, click on the little box with an arrow on it in the bottom right of the Bibliography group on the Endnote tab. The Format Bibliography dialog will be shown.

Change the temporary citation delimiters to your required symbol and click OK.

Now, in the document, unformat the citations. They should appear with your new temporary citation delimiter around them.

Then click on Update Bibliography. The extra visits to the Find Reference dialog should be avoided, this time.