Tag Archives: reference management

A reference management strategy that works

Sick of thinking “I know I read something about x somewhere” and having no idea where to start looking for that elusive x? The frustration! Here’s how I’ve overcome this problem.

For me, no single reference management software package suited my needs. So I use a combination of Endnote and Mendeley Desktop. Why? Because:

  1. References generally move from Web of Knowledge (WOK) to Endnote pretty accurately and easily. And Endnote works brilliantly with Word. It’s so easy to change the referencing style you want to use; not just to another journal style, but you can customise a particular style to your needs (eg if the journal stipulates you need a full stop after each initial but Endnote hasn’t done that, it’s pretty easy to customise the style so it does). References DO NOT migrate from WOK to Mendeley well at all. When I initially trialled Mendeley I found it incredibly frustrating because every reference needed a complete overhaul. I have no idea how well Mendeley works with Word – I never got that far!
  2. But…. Mendeley has an absolutely awesome feature that Endnote is lacking. When you do a search in Mendeley, it not only searches the text that makes up your reference (eg the title, author, abstract, notes). It also searches WITHIN every pdf. That’s right – Mendeley searches the full texts of your entire pdf library. So next time you think “I’m sure I read something about perimeter:edge ratios/”we must not let a forest full of trees fool us”*/glucocorticoids“, just stick the word or phrase into Mendeley and it will save you HOURS of searching time. Trust me. This tool is a god-send.
  3. Mendeley has some other cool features that Endnote does not. Like marking favourite articles and marking articles as read or unread (great for motivation as you see more “read” articles accumulating). Mendeley also lets you view the pdf and your notes at the same time, making it very easy to take notes while reading. Both Endnote and Mendeley let you use tags/keywords/groups, but to be honest, I haven’t needed these since being able to search within the pdf files.
  4. I can take my Endnote/Mendeley Desktop combo out to the field where there’s no internet access. This was a key criteria for me.

An outline of the process I follow:

First, I mostly use WOK to find articles. This platform has a really simple process to export references to Endnote. When I export a reference from WOK, I also save the article’s pdf file into a designated folder on my hard drive.

Once every few weeks, I tidy up my Endnote references and export them to Mendeley. To do this, I simply:

  1. Work from the group on the left of the Endnote screen called “Unfiled”.
  2. Open the first Endnote reference and also open the corresponding pdf file. Check the required Endnote fields have been populated correctly. Usually I find they are okay. The things I need to really watch out for is a) some article titles get imported as ALL CAPS, and b) unusual letters with accents and umlauts don’t import (eg András Börger would incorrectly be entered as Andras Borger).  You can look at the authors displayed on the pdf file to see if their names contain unusual letters. To help with correcting the letters, I also maintain a basic Word file with most of the unusual letters I encounter. This makes it easy to copy and paste the odd letter from Word to Endnote.
  3. The pdf file is then attached to the Endnote reference. I can then delete the pdf file from its location on my hard drive.
  4. Steps 1-3 are repeated for all the references in the Unfiled group.
  5. I then click File/Export to export all these updated references as an XML file.
  6. Open Mendeley and click File/Import/Endnote XML to import the references into the Mendeley database.
  7. All the imported files initially sit at the bottom of the list of references in Mendeley. It’s really easy to quickly run down each one and type either “Paper copy on file” or “Have not yet printed a copy” in the notes section for each reference. I tend to print out pdf’s for articles I definitely want to read (I find it a little easier on my eyes to read from a paper copy). Articles that look kind of relevant or that I might want to read down the track are just kept as electronic pdf’s. Having this note in Mendeley stops me from inadvertently printing out the same article multiple times.
  8. Finally, in Endnote, I move all the “Unfiled” references I just imported to a group I’ve called “Imported to Mendeley”. This keeps them separate from future unfiled references and I don’t end up importing references twice (although this isn’t much of an issue since Mendeley picks up on duplicated references).

I keep all the notes I take from reading the articles on Mendeley (if I haven’t yet done the Mendeley import at the time of reading the article, I can put the note in Endnote and it will transfer over at the time of the import).

The process may sound involved, but once you get the hang of it, it’s pretty straight forward and not very time demanding. You get to exploit the strengths of both programs and avoid the weaknesses. Endnote costs a little (although I got a free copy from my university), while Mendeley Desktop is free. So next time you’re sitting there swearing at your computer, have a think about making the switch. Did I say Mendeley searches the entire texts of your pdf files? Give it a go!

* The full quote is “We must not let a forest full of trees fool us into believing all is well” from Redford (1992). It was later cleverly used by Stevens & Watson (2013).

Redford, K. H. (1992). The empty forest. Bioscience 42, 412–422.
Stevens, H.C., Watson, D.M. (2013). Reduced rainfall explains avian declines in an unfragmented landscape: incremental steps toward an empty forest? Emu 113, 112-121.