Zotero: deep PDF links

Dear Community,

Is there any way to create links to annotations in the built-in PDF reader of Zotero 6?

At the moment, I can create links to items with the help of zotxt but how about markdown links to the PDF annotations/notes?

I could add all annotations to a note using “Add Item Note from Annotations”, and export the resulting note in Markdown format, where I can get a deep link to the annotations. Any chance I could do this more straightforwardly? e.g. “Copy Selection and Link” as in Bookends?

CleanShot 2023-04-14 at 22.38.42@2x

Welcome to Hookmark forum, @AskMeerkat .
Hookmark relies on Zotero regarding link information. Currently, it seems there is no way for Hookmark to get the link info.

Welcome to the Hookmark Forum , @AskMeerkat. Another approach is to open the zotero PDFs in Skim, and deep link from there. You’d want to make sure, however, that Zotero doesn’t mangle your PDFs in its sync or other operations. Having said that, I’d prefer Hookmark leverage a Zotero API or a Zotero extension .

Hi @AskMeerkat I use Zotero as well, Zotero forum might be better place to ask, the topic of linking to specific annotations if this is what you are asking (not specific to Hookmark) was discussed in several places

hen you export annotation to note, a file is create under Zotero item, in general currently link by zotxt is provided to Zotero item, not to pdf or note

zotero create link to annotation like the one from Zotero forum discussion

“Hearing loss is the most common sensory disorder in humans with an incidence of approximately 1 in 1,000 children.” ([Hsu et al., 2005, p. 36](zotero://select/library/items/A8L8GE69)) ([pdf](zotero://open-pdf/library/items/PMUKHI63?page=1&annotation=WUPKUYJX))

this could be accessed probably by Zotero API, but I dont know about any plugin that do that know and can be connected to hookmark

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maybe if some of us contacted the author of the “zotxt” Zotero extension he would be willing to investigate support for deep linking…

Otherwise might be easier to convince Zotero developers to provide a “hook” that Hookmark can use in more straightforward manner, (like “copy link to annotation” in the dot menu for specific note in the left sidebar or directly from note, + keyboard shortcut) - link then go directly to place in pdf where the annotation was made

This might use the link that is already strored/created in Zotero annotation database

Might be useful n to more than MacOS/hookmark user :slight_smile:

here is another recent discussion about linking to annotations monitored by Zotero devs


Many thanks @echej for sharing your info and experiences. Yes, Zotero does create a link (or an ID) for the annotation as shown in your reply, but that ID is only accessible after going through the process of:

Add Item Note from Annotations in the PDF reader → Locate the note → Export Note → Select Markdown format and include Zotero links.

It would be much more convenient if this can be achieved by a simple keystroke. I believe that magic keystroke should not be difficult given that we do have a way to get the link (though through multiple steps), unfortunately, my skills are shy for such magic :rofl:.

Many thanks @LucB, I’ll have a look at Skim.

This would be so helpful and I do believe it is doable given that the links to annotations are possible but they are only accessible after adding the annotations to a note and exporting the note in markdown.

And this sounds promising :innocent:

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Following my initial question, it turns out this is much easier than imagined. Just focus on the annotation and press Command/Ctrl + C in Zotero PDF reader, the annotations and notes (if any) with deep links are copied to the clipboard. The trick is on the pasting part, you will need to paste the text as plain text to be able to see the links. For text editors that paste text to plain text by default, the markdown links are immediately available (e.g. like below), one can even use drag and drop to do this, whereas for editors like Agenda or Obsidian, pasting as plain text is needed.

“All patients had a complete ophthalmic examination including ...” ([XXX et al., 2016, p. 111](zotero://select/library/items/MGZ4JFEN)) ([pdf](zotero://open-pdf/library/items/WFQLFARS?page=2&annotation=5B8HC5QX))


This is pretty useful. I didn’t notice this trick!

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Awesome, thank you!

If anyone happens to want to do a video of the steps, and share it with the community, that would be grand. Otherwise I’ll try to get to it and put it on our YouTube channel. I’m not a Zotero user myself (except I sometimes use it for importing stuff , based on The best of both worlds: Use Zotero to import references into Bookends by Ryan Ryan J. A. Murphy’s – Ryan’s a Hookmark user too.))

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