Zotfile - Zotero version annotations is crippled.

Since Zotero version 6 now extracts annotations from pdfs, this feature of Zotfile doesn't work for the new Zotero. But the Zotero version is crippled - while it allows you to click on the annotion to link to you back to the pdf, this only works within Zotero. With the Zotfile annotations, you could copy that annotation elsewhere (e.g. a word document) and the link back to the pdf still worked.
Thus, since the Zotfile annotions feature works better than the new Zotero one, how can I turn on that Zotfile annotation feature in the new Zotero version?
Thanks, Vilis
  • edited June 23, 2022
    Zotero annotations include Markdown links back to the item and PDF when you copy plain text.

    The rich-text output doesn't yet support links back, but that will be added as an option soon. It's not the default because rich-text output is more likely to be used in places where a link back to a local Zotero installation is inappropriate (e.g., a blog post), and it's much less clear than in plain text what the link actually is.

    ZotFile is no longer maintained, and its annotation functionality was redundant, so it was removed. Zotero's annotation functionality is much more powerful and flexible than ZotFile's was (integrated UI options, direct linking to annotation positions, toggleable highlight colors, note templates, customizable back-links, active citations in word-processor documents, restoring of removed citations, etc.).
  • This is good news that Zotero will allow me to copy the annotation links (when copying plain text). Now to figure out how to do it.

    When I copy an annotation from Zotero, then in Word I have several options for pasting (Unformatted Text, HTML Format, and Unformatted Unicode Text). None of them give me links. Or is there some other way of copying from Zotero?
    Thanks, Vilis
  • How exactly are you trying to copy? Currently, the links are included when you copy annotations or highlighted text directly from the PDF reader, and pasting that as Unformatted Text into Word includes the Markdown links for me.

    If you just copy from the note editor, you just get the visible text. We could consider transforming the embedded annotations/citations in the same way when copying from there, but it'd be a bit weirder — e.g., you might not have the entire annotation or citation selected, and then what's the correct behavior? So right now it just copies the actual text that you select. We could maybe perform the transformations as long as the entire annotation/citation is selected.

    But generally people are either copying specific annotations directly from the PDF reader, which copies Markdown with links, or they want the full contents of the created note, in which case they either use some sort of integration plugin (e.g., the one that exists for Obsidian) or export the note to Markdown. You can do the latter — right-click on the note, export to Markdown, and load or paste the file into Word.
  • I am not using the Zotero PDF reader - I'm using another reader (that also does PDF editing).
    Yes, I am just copying from the note editor. That is what used to work with Zotfile.
    I've now just tried exporting to Markdown. When I place that into Word, the links aren't there. Even if that would work, it is a laborious multi-step process - it would be so much easier to just copy the annoation text from Zotero and then paste them into Word.
  • edited June 24, 2022
    I've now just tried exporting to Markdown. When I place that into Word, the links aren't there.
    I'm not sure what you mean by that. If you add annotations (created in Zotero or elsewhere) to a Zotero note using "Add Note from Annotations" and export the note to Markdown with "Include Zotero Links" enabled, you'll get Markdown links back to the item and PDF in the note, which you can see by opening the .md file in any text editor.

    If you're not seeing that, you'll need to explain exactly what you're doing, step by step, since this certainly works.
  • After exploring this some more, I can eventually use the link - but the process has many steps.

    Yes, I see the link, but cannot use it directly. For example, when placing the Markdown export into Word, at the end of the annotation I see:


    I assume this is the link. When I click on it nothing happens. So I try copying it, and inserting this as a link in Word (using Insert/Link). Then it becomes clickable, and I can access this using Ctrl-Click.

    Is there an easier way to do this? With Zotfile I used to be able to just copy the annotation text and paste it into Word.

    Thanks, Vilis
  • edited June 25, 2022
    As I say, we'll be making it possible to include links in the rich-text output soon.

    Most people aren't doing this in Word — it's in Markdown editors where they want links back to the PDF — so it hasn't come up much since we launched Zotero 6.
  • As a start, in the Zotero Export to Markdown, allow Export Markdown to the clipboard.
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