Reference Management

Researchers “stand on the shoulders of giants“, which in practice means reading a lot of academic papers and reports.  Lots.  You not only want to read them, but also cite them in papers you write, search them, and organise them by whatever topics you’re investigating.  How do you do that?
When I was a PhD student, I kept hard copies of the papers I read, and a collection of bibtex files containing reference information.  The bibtex files were separate, each on a different topic.  Since getting back into research in 2004, I’ve gone digital and have tried a few solutions: Reference Manager, EndNote, bibtex again, and zotero.  After each one, I kept reverting to my clumsy manual approach: storing PDF documents in directories, with each directory representing a topic.  Often, papers relate to more than one topic – sometimes then I put a copy or soft link in each topic directory.  I said it was clumsy!  But at least I can work when I’m travelling and off-line.
As a result, I now have dozens of directories stuffed with thousands of PDFs.  (I have less than three thousand, but a colleague has more than ten thousand.)  These calcified directories represent a fixed collection of topics that, as my research focus evolves over the years, is increasingly inappropriate.  I suspect a lot of people work like this.
So I’ve been delighted to discover Mendeley Desktop.  It’s still in beta, but I like its approach.  It lets me keep my PDFs as they are, and works with me to index them and import their bibliographic information into a database, using text recognition and bibliographic web services.  The quality of both of those mechanisms are a bit patchy right now, but it has “needs review” status tracking so I can manually check and correct that bibliographic data over time.  What’s also cool is that I can tell it to “watch” my directories – if I dump more PDFs in there, it’ll incrementally import those too. Mendeley has all the normal features: reference-importing bookmarklets, exporting in bibtex/whatever, Word and Open Office plugins for creating reference lists, etc.  And of course it also has tagging: so now I can create tag topics for my references – organised into as many overlapping topic areas as I need.
I feel like my reference collection has opened up to me, and is becoming a much more useful resource.  That’s fun and exciting but I have to make sure I don’t spend so much time organising my references that I end up not actually doing research!