How do I work with Zotfile and Zotero to extract Skim annotations? It won't work for me...

As the title:

I'm a newbie to Zotero, but I've added a few webpages (using the Zotero browser plugin) as well as a few downloaded PDFs to my Zotero library. I use Skim to highlight some passages, then return to Zotero, right click and choose "Manage Attachments->Extract Annotations". Zotero puts up a little dialog saying Zotfile is doing that, then after a moment the dialog disappears. And that's it. Nothing has been extracted. I am using a Mac, 10.12.4, Zotero 5.0.30, Zotfile 5.0.6, Skim 1.4.30 (104).

Another unrelated question: if I add a PDF directly to the Zotero library, I am told Zotfile can't extract annotations because it's a top level item -- so I right-click and do "create parent item". Why is this necessary? Am I doing the right thing? (Even when I do this, I still can't extract annotations, as per above)
  • Extract annotations doesn't work with Skim, which stores PDF annotations in a non-standard format.
  • Regarding your second question, when Zotfile extracts annotations (which requires they be stored in the Standard PDF format—as is done by Preview, Acrobat Reader, and most other programs, but not Skim), it attaches the annotations as a note to the PDF's parent item. Notes can't be attached like that to a bare PDF file in Zotero. In general, you always want to work with regular Zotero items (not bare PDF files) in Zotero, as this opens up most of Zotero's features (searching, sorting, generating citations, etc.).

    See here for more details on getting items into your Zotero library:
  • edited December 6, 2017
    Thank you @bwiernik and @adamsmith -- @adamsmith: what programs (other than Preview) would you recommend that work with Zotfile-- that is, that show some more power than Preview, like the ability to add various types of notes, but still store notes in a standard format? (Or is this a contradiction in terms?). I'm trying to find a good workflow to manage my PDF annotations so that I can use them in writing my papers. I'm looking into qiqqa, for example and wonder now whether that's compatible with Zotfile.

    On an unrelated note: is there a way to export a citation from the Zotfile link? That is, if I want to export a full citation including the page number of annotation (which I realize may not be accurate, since it's counting from the beginning of the document), is there an easy way to do this similar to the "quick copy" of the citation without the page number (in the main Zotero window)?
  • Adobe acrobat is probably the standard tool for this.
    Qiqqa is closed source and uses its own system to manage notes (it also hasn't seen a lot of uptake, so I'd be very worried about sustainability)
  • I’ve tried a lot of PDF programs on Mac and have only found Adobe to be reasonably stable and use the standard annotation system. The free version has most features you are likely to need.
  • edited December 6, 2017
    Your notes in Skim-pdfs are not lost to Zotfile. You can export the respective files from Skim, chose the pdf option and tick the box "With embedded notes". PDFs treated in this way will adhere to the general standard for notes in pdfs and will be picked up by Zotfile. Make sure to work on a copy if you wan't to continue using Skim - pdfs treated in this way will lose editability of notes and highlights from within Skim. (You will however be able to edit them in Preview or Acrobat.)
  • I am in the same boat and have written a Python script that can be used to semi- and fully automatise the conversion of Skim annotations to standard PDF annotations on Mac OSX.

    There are several options how you can execute the script. One is by using Alfred Workflows ( as a wrapper: You would select one or more PDFs you want to embed or unembed Skim notes and hit the Alfred shortcut. The script will then process the PDFs. You can embed and unembed the Annotations as you like. I haven't seen any errors during the conversion in my tests.

    A second approach would be to wrap the script in an Automator workflow and then attaching the workflow to a folder as a folder action. This would automatically run the script whenever a file is added or changed within the folder.

    The script also has a method for batch processing pdf files in a folder with nested subfolders. The performance is quite good: I have used it to embed Skim notes of 568 pdfs scattered in a folder with various subfolders. It took 5 minutes in total.

    You can have a look at the script at
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