Managing references

As some of you are aware, I had a little hiccup with my reference management while I was writing my comprehensive exams. Unfortunately, I did not take my own advice, and tried out a new tool for an important time-sensitive paper. Fortunately, I had a back-up plan that saved me.

What I really need is:

• A way to keep all my annotated PDF files organized. I'm file inept. Keeping things in folders doesn't work for me. I cannot consistently label things, and when I am looking for something, I want an easy way to find it. Also, I found that many of papers belonged in more than one category – but keeping multiple copies means that annotations get lost or misplaced and managing multiple copies is a pain. Search-ability is critical – I need to be able to find things when I'm looking for them.
• A place to keep my notes. Even though I like to keep my notes with the annotated files, I also find that when I'm doing a literature review, I like to keep all my related notes in a single file.
• A way to automatically generate my reference lists in papers. I'm a big believer in "cite while you write", that is, as I draft my paper I place my citations (at least most of them, occasionally, I'll just write stuff done and put in a note to find a reference).

My current solution to this problem involves three different software packages – one for each item.

For item 1, I use Mendeley. Mendeley lets me drag-and-drop annotated PDFs. In many cases it automatically finds all the information I need for referencing, and when it doesn't it has an integrated search function. I can create virtual folders to categorize my documents, and I can even create shared folders to share my reference lists with others. In addition, the search function in Mendeley works very well – it searches both my notes and inside the PDFs themselves. I blogged about Mendeley in a post on my inability to file things, and I extoll the virtues of Mendeley here; however, this was written before I discovered scalability issues when trying to use Mendeley for item 3.

For item 2, I use Microsoft Word. I find that I want all my related notes in one document, so I just dump them into Microsoft Word. When I do I literature review, I find the process to be similar to coding qualitative research results. I put all my notes and reflections into a single Word document, and then code it and draw up a conceptual framework.

For item 3, I use Bookends. I had tried to use Mendeley for this, but ran into scalability issues with the Microsoft Word plug-in. I submitted a bug report to the Mendeley development team, and they have now contacted me to tell me they are going to fix the issue; however, it took them several weeks to reply. I was working on a time critical paper, and needed something that just worked. When Microsoft pushed an update that broke the Bookends scripts, I posted a message to the message board and the developer responded within a day (given it was a weekend, I was impressed). Fortunately, I was able to work around the bug, and get things working again. Bookends works, is very scalable (works well on long papers with lots of references), and the developer is very responsive. Sorry PC folks, Bookends is a Mac only product.

So, there you have it. The three different tools I use to manage my references. It's a bit clunky, but it is working for me. What tools do you use?