Yet another PDF annotation question; Zotero use


I’m new to DT, and I’ve spent the past few days trying to figure out if the program is for me. I’m a doctoral student trying to get good structures in place for beginning dissertation research. Part of the problem is that I’m rather invested in zotero, and I’d like to continue to use it to manage my pdfs and bibliographic data (I’ve decided that zotero’s limited search options and reliance on tagging and manual identification of “related items” is just too cumbersome to use). My solution has been to open pdfs in zotero, and place indexed copies of pdfs in relevant research folders as I work. Annotations that I make to the pdf show up in DT, which is nice (though I’m a bit worried about having hundreds of broken file paths if I ever have to move my zotero database or they change their database structure; advice on that?). I’ve given my pdfs in DT filenames that indicate what the content of the document is.

My problem, like so many others, has to do with having DT index my pdf annotations. Instead of relying on keywords that DT recognized in my file names, I’d like to have it search my actual notes. I understand that version 2 will have support for Skim, and so all will be well. For now, however, I’m annotating pdfs in Acrobat 9, and I have hundreds of pdfs already annotated in Acrobat. I’d really like to be able to search these annotations.

I’ve learned through other posts that Acrobat does not save its annotations in the text layer, which is why notes made in it are not indexable or searchable right now in DT. But will this change?

A few people have said that you currently can search pdf annotations made in Preview, and I’m willing to go from Acrobat to Preview for now, if it is a solution. But after a number of tests (and synchronizations), my Preview-made annotations are not searchable, either.

So, long story short: is there any way to annotate pdfs right now and have them searchable in DT? Are there any scripts that might render my Acrobat annotations searchable either now or in the future?

I realize that some of my questions touch on issues discussed in various forums, but after hours of reading and searching, I haven’t been able to find a straight answer to most of these questions. This post ( is about the closest thing, but it refers only to future implementation of PDFKit, which Acrobat, as I understand it, is not.

Many thanks.