iBooks is built without AppleScript support so I'm still using iTunes to manage my PDFs. But if you need to programmatically add a filelike a PDFto iBooks you can use this trick, where filePath is an alias:
using terms from application "iTunes"
tell application "iBooks" to open filePath
end using terms from
Unfortunately, you can't edit the tags in iBooks. Nor does iBooks seem to use any existing PDF metadata except "Author". Strangely, in fact, it uses the PDF's file name (without extension) for "Title" instead of checking the PDF's metadata for "Title". And while I'm making wishes, "Keyword" metadata could be parsed for a Category and perhaps a way could be found to use the PDF "Subject" metadata as a description tag somewhere.
iBooks, which seems to me to be a pretty basic database manager, stores much more metadata for other types of books (have a look at ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books and the Books.plist there) so it doesn't seem like it would be much of a bother to accommodate PDFs a little better.