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.

Converting a Text Bibliography to Endnote

This is a perennial favourite question that I am asked, and there simply is not a good answer: ‘All my references are in a Word document. How can I convert them to Endnote?’

I have found, however, some new (to me, anyway) methods of trying to sort this problem out.

There are some instructions here:

http://libraryguides.missouri.edu/content.php?pid=89799&sid=671253

The instructions refer to WizFolio, yet another free (or, in this case, semi-free) online bibliography reference manager, to be found here:

http://wizfolio.com/Default.aspx

Endnote to Latex Transfer

Peter Robejsek very kindly send me an email recently outlining a problem he had, and a solution he came up with, to transfer a Word document with Endnote references to LaTeX using an applescript?

Since at the time I had a fairly large (100+ pages) document already written in Word and wanted to transition to LaTeX I faced the problem of having to replace all the citations. Obviously doing this manually would have been terrible, so I wrote a bit of AppleScript to automatize the whole thing with the help of Excel.

I thought it might be useful for others as well especially given the large number of Mac users these days. So if you would care to publish it on the blog, please do so (if not, that's also fine). The code is not very polished since I had never written any AppleScript before and I am sure the whole strategy could be improved but back when I worked it out I was looking for a quick rather than an elegant solution.

So, here is the description and the script below in plain text. Any comments, please let me know.

This document gives a step by step procedure how to go about exporting a library from Endnote into JabRef and using that to generate BibTex. In the second part (steps 3 & 4) we show how to take an existing word document with Endnote bibliography and replace the references automatically by LaTeX code references. It is assumed that the natbib style is to be used with LaTeX and that the user is on a mac operating system.

1. Endnote
Need to get Endnote Reference Number, Author first name, date and Bibtex key into the same excel spreadsheet
a) start with Endnote. Here create an export output style (e.g. go to the finder, Usr/Applications/Endnote/Styles/BibTeXExport.ens and create copy; Rename to BibTeXExportToJabref.ens or something like that)
b) In Endnote go to Edit->Output Styles->Open Style Manager and select the newly created output style
c) In Endnote apply the new output style to your current library and go to Edit->Output Styles-> edit"new output style"
d) For every entry in the Bibliography.Templates category add another field like "|   `endnotekey = `{Record Number}" as well as a "," after the preceding field entry. The result will look like this:
…
|   `keywords = `{Keywords},
|   `year = `{Year},
|   `url = `{URL},
|   `endnotekey = `{Record Number}
e) Export this file from endnote as a .txt file using your newly created output style.

2. JabRef
a) add "endnotekey" field: Go to Options-> Set General Fields and type into the line beginning with "general": ";endnotekey"
b) make the field visible in Jabref: Options -> Preferences -> Entry Table Columns -> add field "endnotekey"
c) Autogenerate BibTex keys. The resulting library file will be used with LaTeX
d) also avoid having the url and note fields show up in the bibliography by going to Tools->Set/Clear/Rename Fields and set all fields to " " with overwrite active.
e) create a copy of this library file. When that is done open in JabRef and rename the "endnotekey" field. This is necessary so that its contents can be exported to *.csv. This is done by: Going to Tools -> Set/Clear/Rename Fields and renaming the "endnotekey" field to "note". This will transfer the Endnote Reference Numbers to the field note. Some entries in the database may already have text in "note" however. In this case this needs to be deleted first: Tools -> Set/Clear/Rename Fields-> Clear Fields+overwrite existing values.
f) Export the .bib library as a .csv library

3. Excel
a) import the *.csv library into excel. Delete all columns except for "Identifier" (=Bibtexkey), "Author", "Year" and "note".
b) assuming the fields remaining are in the order as above with one header row, enter the following formula in E2: =LEFT(B2;SEARCH(",";B2;1)-1. This should obtain for us the last name of the first author.
c) Then enter this formula into F2: =CONCATENATE("{";E2;", ";C2;" #";D2;"}"). This will give us the same format as an unformatted Endnote citation. also into G2: =CONCATENATE("{";E2;", ";C2;" #";D2;"@@author-year}") to get the endnote formatted author year style. Also in J, K and L =CONCATENATE("{";E2;", ";C2;" #";D2;";"), =CONCATENATE(E2;", ";C2;" #";D2;";") and =CONCATENATE(E2;", ";C2;" #";D2;"}") to get the cases where there are "mass citations" i.e. more authors in one set of brackets.
d) Enter into H2 the corresponding format for Latex that goes with F2 (i.e. gives author comma date in brackets): =CONCATENATE("\citep{";A2;"}") and into I2 the corresponding format for Author (date): =CONCATENATE("\citet{";A2;"}"). Now fill down cells E to I. Corresponding to the mass citation case enter in M, N and O: =CONCATENATE("\citep{";A2;","), =CONCATENATE(A2;",") and =CONCATENATE(A2;"}") respectively.
e) then take these cells and paste special (value) them to columns P-Y, make note of the number of rows. (Note: In case you notice any weird symbols e.g. ş gets translated as Yue or something of the sort, you need to search and replace these before doing step e) in order to be sure that no citations get left behind)

4. Word
a) Go to Tools-> Endnote X5 -> Convert to unformatted citations. Select the entire text you want to get your endnote citations replaced in (cmd+a).
b) run this applescript where the to value should get replaced by the number of rows from 3.e)
repeat with theIncrementValue from 1 to 345

    repeat with theIncrementValue from 1 to 345

      tell application "Microsoft Excel"

       set rg1 to "P" & theIncrementValue

       set rg2 to "Q" & theIncrementValue

           set rg3 to "T" & theIncrementValue

       set rg4 to "V" & theIncrementValue

         set rg5 to "U" & theIncrementValue

       set EndForm1 to value of range rg1 as string

       set EndForm2 to value of range rg2 as string

         set EndForm3 to value of range rg3 as string

       set EndForm4 to value of range rg4 as string

            set EndForm5 to value of range rg5 as string

   end tell

   tell application "Microsoft Excel"

            set rg6 to "R" & theIncrementValue

       set rg7 to "S" & theIncrementValue

            set rg8 to "W" & theIncrementValue

       set rg9 to "Y" & theIncrementValue

            set rg10 to "X" & theIncrementValue

            set TexForm1 to value of range rg6 as string

       set TexForm2 to value of range rg7 as string

         set TexForm3 to value of range rg8 as string

       set TexForm4 to value of range rg9 as string

            set TexForm5 to value of range rg10 as string

  end tell

   tell application "Microsoft Word"

       set findRange to find object of selection

            tell findRange

                  execute find find text EndForm1 replace with TexForm1 replace replace all

                  execute find find text EndForm2 replace with TexForm2 replace replace all

                  execute find find text EndForm3 replace with TexForm3 replace replace all

                  execute find find text EndForm4 replace with TexForm4 replace replace all

                  execute find find text EndForm5 replace with TexForm5 replace replace all

            end tell

   end tell

end repeat

Please note: The above procedure does not account for names that are of agencies (European Banking Authority etc.) however the vast majority of quotations should be easily taken care of in this way.) Feel free to improve on the approach as desired.

Applying these steps worked well for me at the time of writing. However I can give nor warranty explicit or implied that the approach is fault free. The only application took place on MacOS X 10.6.8. Always back up important files before manipulating them!


 

Mac Os X 10.8.2 Update

As Mac users may know, there have been issues with Os X 10.8.2 and Endnote not getting on with each other. The new Os release has seemingly made Endnote freeze from time to time.

There is now a new release of Endnote X6 for Macs (X6.0.2), which is supposed to cure the problem.

As this is a Mac specific problem, there is no corresponding Windows update, so the latest version for Windows remains X6.0.1.

Citing more than one article in the text and prefixing the last article with 'and'

"I want to be able to cite 3 articles in the text with commas between the first two and "and" between the 2nd and last. As for example (Smith et al, 2002, Jones, 1999 and Bloggs, 1986). How can I do this?"

Firstly, you need to set up the multiple citation separators to use commas; by default this usually uses semi-colons.

Multiple citation separator control is at the bottom of the Citations Template area. Insert a comma, and remember to add a space afterwards.

To add the “and” before the last cited item is more difficult. There is a way to do this but it has to been to done to each citation when they have been created in Word. It cannot be done through the output style on EndNote.

In Word make sure the cursor is in the required citation.

From the toolbar choose Edit citations (or right click with the mouse).

An edit box will appear with all three citations displayed.

Click on the last citation and then click in the prefix box.

Type 'and' then a space.

Click on OK. This will allow the word to appear before the last citation. Unfortunately the comma appears as well, but at least this does allow the and to be added manually, as desired.