Beta: Consolidating Mendeley proprietary annotations into open-format PDFs without exporting

Hi everybody,

This beta has been amazing so far. Congrats on the great work, as it probably involved some serious reverse-engineering.

I realize that we can now see proprietary Mendeley annotations within the new built-in PDF reader, and that we can bulk-export them to normal annotated PDFs any viewer/editor can open. (And with much better results than those provided by the old Mendeley export tool from years ago.)

However, is there a way to bulk-convert the PDFs without exporting them so that they stay in place? Meaning, making it so that a Mendeley PDF that is attached to an item in the Zotero library becomes an "open-format" PDF including the annotations, without moving it elsewhere and having to re-import it again?

Maybe I'm missing something and it's super easy, so I apologize and thank you in advance!
  • Mendeley isn't really relevant here. Zotero imports Mendeley annotations as Zotero annotations. Once they're in Zotero, they're the same as any other annotations you create in Zotero itself. As noted in the preview announcement, there are good reasons for that: "Annotations are stored in the Zotero database, not in the PDF file, which allows for much more advanced functionality as well as fast syncing."

    We've said that it will likely be possible at some point to transfer Zotero annotations to the PDF file and remove the source annotations, and vice versa, but once they're in the PDF they'd be read-only annotations like any other external annotations. Unless you have a very good reason to do that, we'd recommend simply exporting the files as needed (e.g., when emailing to someone). Unlike with Mendeley, there's never any doubt that you'll be able to get your data out of Zotero in whatever form you want.
  • Okay, it’s great that it will be possible at some point, just for interoperability reasons to work seamlessly between platforms, because Zotfile doesn’t seem to be able to extract the new annotations and highlighted content either.

    Thank you!
  • Sorry, I meant the highlighted text. The annotations do export fine with the built-in option. But if I rename/move a PDF using ZotFile (Manage attachments > Rename attachments), it seems to get rid of the highlighting.

    I understand it is now stored in the database and somehow gets lost in translation when moving the PDF file (?). This only happens when it does move it. Text highlighted in the new location does stay highlighted even after renaming again.
  • It gets lost because under the hood Zotfile deletes the attachment item and makes a new one. Zotfile hasn’t been updated to accommodate the new PDF reader, and updating it would likely require a major overhaul. I would personally recommend stopping using Zotfile to move PDFs and just let Zotero manage their location.
  • Makes sense, it's what I was guessing. Thank you!
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