Zotero Beta and iOS annotation app - saving native PDF annotations to actual file

DoubleLayer · August 10, 2021

I am happy to be a beta tester for the new iOS app. Making PDF reading available on the iPad is a huge deal for the Zotero platform. However, one of my favorite things about Zotero is that annotations were made natively. All annotations get saved directly to the PDF so if you send the PDF to others they can see the annotations no matter how they read the document.

In my experimentation with the new annotation tool in both the iOS app and in Zotero Beta on Desktop, annotations created within the app are saved to the Zotero database, not to the PDF itself. Both apps can read annotations already saved to a PDF, but new annotations do not appear on the document proper.

Is it possible to save annotations as native PDF annotations? Alternatively, is there a way to open and edit a PDF in your library in another PDF editor on the iPad like PDF Expert that does allow for annotations directly on a PDF?

dstillman · August 10, 2021

You can export PDFs with standard annotations embedded from the File menu in the desktop app (either Export PDF…" in the library view or "Save As…" from the PDF reader) or via the Share sheet in the iOS app.

DoubleLayer · August 10, 2021

Thanks for the reply. I actually just found the export feature yesterday after posting this comment and it does a good job of exporting as native annotations. However, I still think there is benefit to having the annotations saved as part of the PDF itself and synchronizing them that way. It makes it very easy to open the file in a different PDF reader and manipulate or interact with the annotations that you've made in Zotero while still keeping all the changes synchronized. This is useful for example if there is a different application that has particular features you want that may not yet be available in the Zotero annotation tool.

dgrobinson · August 11, 2021

does saving the annotations separately from the pdf make it possible down the line to enable a library wide annotation search , at least for annotations made using the new system?

dstillman · August 11, 2021

@dgrobinson: That's planned. We'll try to support it for embedded annotations as well, but it's certainly much more straightforward and efficient with annotations stored in the database.

dstillman · August 11, 2021

@DoubleLayer: We may make it possible to do a manual conversion of Zotero annotations to embedded annotations while keeping the attachment in place so that you can open the file in another reader, but it's not going to be the default — there are many reasons for the switch to externally stored annotations. To quote what I've said elsewhere:

Zotero is a lot more than a dedicated PDF reader, and there's functionality we want to offer that's not supported by standard PDF annotations (e.g., tagging of annotations). Storing annotations in the DB also allows for much faster syncing and processing, will make it possible to view and edit annotations in contexts where it wouldn't otherwise be possible (e.g., the web library), and avoids conflicts and lost data when one or more people are editing annotations on multiple devices, which has always been a major limitation of PDFs in Zotero.

If you don't care about any of that, there's nothing stopping you from continuing to use an external PDF reader as you've always been able to. But it will be just as limited as it's always been.

DoubleLayer · August 12, 2021

@dstillman fair enough. I can definitely appreciate that saving the annotations to the database gives you much more flexibility in what additional features you can add. Tagging annotations is going to be an awesome feature.

I would be OK with the ability to embed annotations keeping the attachment in place. It would be great if you could apply it in bulk across the whole library. In fact, if this could be set up to run automatically in the background it would give the best of both worlds because any "standard" annotations would be pushed to the PDF and accessible anywhere but for day-to-day usage you can use Zotero's annotation tool with all the new features you are adding.