Although it is possible to take notes in the Books presented in Ibooks, which is for my purpose a very nice feature this function does not function does not be present in the pdf files. And since 98% of the stuff I use are pdf files (music books) I did not succeed in taking notes within the files. Converting the pdf files into an epub format made a complete mess of the indexing and the size of the sheets so it was no longer possible to select to use the books in a proper way. So I'm stuck. Will there be an update from Ibooks to take notes also in pdf files from Ibooks?
There are a number of apps that support PDF annotation. I use Goodreader, more for reading than note taking, but have heard good things about taking notes in it.
Thanks pogopossum,
I'm using now Goodreader. This has also the advantage of a good interlinking to other available documents.
This is also not functioning with ibooks. Goodreader has some drawbacks compared to ibooks.
You cannot recognize the books easily since no frontpages are present and you need to scroll more to find the correct document. A annoying thing is that once you enlarge the index and jump to a linked page that page will show up in the enlarged fashion. So you always need to resize the new page. This problem is not present in ibooks. An enormous good feature of Goodreader is the easy and many ways to import files.