PDF File naming conventions

I keep an extensive library of PDF files on my computer. Keeping track of these presented me with two problems.

The first problem was how to name the files. I have decided upon a convention that gives me a reasonable amount of information at a glance. My convention yields file names in the following format:

Smith.03.PNAS.102.1194.pdf

Where:

I do not put spaces in the file names. Spaces in filenames can confuse some computer operating systems.

Keeping track of PDF files in your library

Keeping track of PDF files in a library on your computer presents a number of problems. First, they have to be filed in a fairly extensive series of subfolders, since the directory structure on most computer operating systems cannot accomodate hundreds or thousands of files easily. I actually keep two sets of folder: (1) PDFs by Authors; and (2) PDFs by Subject. Within each of these major folders, I have a series of subfolders with names like: A.Authors.PDF or L.Subject.PDF. Within each of these folders, I will have another series of folders with names like Jones, Ken (in the J.Authors.PDF folder), or EBV virology (in the E.Subject.PDF folder).

Papers are usually assigned to a folder based upon the name of the communicating author, especially when I am likely to have more than a few papers from that author.When I am likely only to have a few papers from a lab, I will usually file these under a subject. Finally, I often make aliases of a file so that I can place it in both an Author folder and a Subject folder.

This system is not perfect, but for me it's currently the most practical solution.

Finally, it is possible to keep track of the where the papers are stored in an EndNote database. I use the EndNote URL field, since you can invoke EndNote's Open Link command to directly ofpen the PDF file from within EndNote. The format of the entry in the URL field is something like this:

JDA Office Data HD:Documents:PDF Files: PDF by Authors:N.authors.PDF:Nixon:Aandahl.02.JI.169.802.pdf

Note that you'll need the full path name.

I have to admit that while using EndNote to keep track of thousands of PDF files, in practice this turns out to be a lot of work, and I don't always keep up with it. For me, I find that my structured file system is usually good enough. When it fails, I can always go to the internet to find the PDF file again.