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:
| Smith | the name of the first author |
| 03 | the year (or 2003, but on some computer systems, there is a limit to file name length, so I usually abbreviate it) |
| PNAS | a succinct abbreviation of the journal name (e.g. PNAS, Sci, Nat, JI, NatImm, GD, etc); I try very hard to omit spaces in the filenames |
| 102 | the volume number |
| 1194 | the first page of the article |
| the document type (this is important for some computer systems to know what application to use to open the file) |
I do not put spaces in the file names (and I omit them from compound last names—"von Willebrand" becomes "vonWillebrand"). Spaces in filenames can confuse some computer operating systems. In addition, I do not include diacritical marks that are sometimes found in non-English names, since these make it harder to search for the file.
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). An sample of the directory structure is shown below.
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.
Keeping track of PDF files in a bibliography manager
I use Sente to keep track of my PDF documents, and I cannot recommend it enough. I have written up extensive notes on how I manage PDF files on my page Handling PDF Documents.