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.)
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