How can I copy text from PDF and include the source filename in the pasted selection?

Question

I'm a biologist and frequently cut-and-paste notes from PDFs of scientific articles.  I name all of the PDF articles with their PubMed ID, a short unique identifier (e.g. 19397482.pdf).  When I take notes, I will select a few sentences from the PDF and then paste them into a text editor for later reference. 
Can anyone suggest a method or script that would allow me to paste the copied text with the Pubmed filename included in a single action?  I would want the pasted output it to look something like this, with the filename appended to the end:
Of the transcripts that were significantly different, there was a greater number of transcripts that were down-regulated in the IVC embryos (380) than the number of transcripts that were up-regulated (208).  [20668257.pdf]
This would really help me to properly cite information sources during the writing process.  I know there are bibliography managers that might be able to do something like this, but I prefer to read the PDF articles directly in Preview and select the text as I am reading. 
Thanks very much for any suggestions / ideas.
jjw

Answer 1

To copy and paste in a single action:
tell application "Preview" to activate
tell application "System Events" to tell process "Preview"
    -- Get the PubMed ID:
    get the title of the front window
    set thePubMedID to word 1 of result
    -- Copy the selected text to the clipboard:
    keystroke "c" using {command down} -- ⌘C
    delay 0.25 -- adjust if necessary
    -- Add the PubMed ID to the contents of the clipboard:
    set theNotes to the clipboard
    set the clipboard to (theNotes & space & "[" & thePubMedID & ".pdf]")
end tell
tell application "Notational Velocity" to activate
tell application "System Events"
    -- Paste the contents of the clipboard to the end of the Notational Velocity document
    key code 125 using command down -- ⌘↓
    keystroke return & return
    keystroke "v" using {command down} -- ⌘V
end tell