Well, when it comes to journal articles, the transition from papers to endnote is painless. Papers makes no bones about being geared directly to journal articles, so much of their metadata features take that to heart. For instance, you won’t find metadata such as Publisher, Location, ISBN, or Editors in Papers. But since I also keep book chapters and newspaper clippings in papers as well, I take all of that extra information that I want to keep and stick it in the Notes metadata spot.
To everything over to EndNote:
The first time, when I want to take everything, I select everything in my Papers library and then select File->Export->EndNote XML Library->Complete Library. From EndNote X2 I select File->Import->EndNote Generated XML.
To export only the latest papers (once I’ve done that initial library export), I keep a running tab of the latest papers by maintaining them in their own Collection, I select those new papers then pick File->Export->EndNote XML Library->Selected Papers Only. Importing in EndNote is the same.
Usually, my PDF attachments are correct in EndNote, referring to the Papers attachment folder. I have seen EndNote’s import omit the attachments in the past, but I don’t recall it being to painful to remedy, by reattaching the PDF manually.
Now that the library is moved over, I double check that the reference type (book, journal, newspaper) is properly selected for each entry in EndNote. I then go through the books and newspapers, updating their metadata fields with the leftovers I had previously stuck in the Notes field.
After that, it’s simply a matter of tuning up my citation/bibliography style to fit my dissertation requirements.
For EndNote, I’ve spent quite a bit of time hacking the connection files in order to eke out some semblance of searching utility. JSTOR searching is a non-starter, even with my university’s EZproxy, hence my use of Papers as the primary. Native EBSCO support is a no-go in Papers, and EZproxy searches aren’t really possible in EndNote, but I’ve scoured the internet and stumbled upon a careless university library that accidently published their EBSCO username and password, allowing me to implement a Z39.50 search connection with EBSCO’s academic database. It’s certainly cheating, and against the rules/law/ethics/whatever, but my library wouldn’t release that information and no one is making native searches particularly easy. Nothing like blaming someone else for my own problems.
It’s not a perfect workflow, far from it. But it works. If Papers would implement comprehensive metadata, basic bibliographic formatting and temporary citations, then I would be so very happy. If/when Bookends gets smart with EZproxy and XML search gateways, I’d be very happy too. Until then, I’ve got this sick turkey with lots of makeup on…