PDF annotations and notes not showing up in Note stream

[SarahG236]

Hi all - I'm sure this is going to turn out to be something I'm not doing properly but I've checked the User Guide and searched the forum and haven't found an obvious answer.

I highlight text in PDFs in Bookends (15.1.1; Sequoia 15.3.1) and add notes but nothing shows up in the notes stream. I have the same issue with all PDFs that none of my annotations or notes are visible in the Notes stream, although "Show annotations in note stream" is selected in the context menu.

Some references have what looks like extra information about the article in the Notes pane, but that's it, e.g.:

<p>Accession Number: 43051090; Bullock, Shawn Michael 1; Email Address: bullocks@queensu.ca Christou, Theodore 1;
Affiliation:&nbsp;&nbsp;1: Queen's University, Canada; Source Info: May2009, Vol. 5 Issue 1, p75; Subject Term: THEORY;
Subject Term: TEACHER educators; Subject Term: COLLEGE teachers; Subject Term: TEACHER training; Subject Term:
PRACTICUM supervision; Author-Supplied Keyword: new teacher educator; Author-Supplied Keyword: pedagogy; Author-Supplied Keyword: philosophy of education; Author-Supplied Keyword: practice; Author-Supplied Keyword: practicum supervision; Author-Supplied Keyword: theory; Number of Pages: 14p; Document Type: Article</p


In addition to fixing whatever I'm doing wrong here, I'm also wondering if there is a way to export only the notes and annotations for a PDF? Right now I do all this highlighting etc and I'm also taking notes elsewhere but if I can export these notes that would be a lot more efficient

Thank you for your help!
Sarah

[Jon]

This is true for all PDFs? Or just some. Depending on how the data are represented internally, sometimes it's not possible to get the content of a highlight (sometimes you'll see the same thing in Preview). If it's just some PDFs, feel free to send one or two to support@sonnysoftware.com and I'll take a look.

As for annotations, have you looked at File -> Notes and PDF Annotations? It's highly configurable.

Jon
Sonny Software

[SarahG236]

Hi Jon, thanks for getting back to me so quickly.

None of the PDFs show highlighted text in the notes stream. Some of them show partial content of the notes I've personally added to those highlights, but not the full note. I'll send over a couple for you to see.

There's no menu item for Notes and PDF Annotations in the File menu for me - there is one for File->Extract Notes and PDF Annotations-> Configure then Extract, which I'll add as a screenshot below but I'm not seeing anything there that would obviously make a difference

Screenshot 2025-03-03 at 11.58.34 AM.png (162.73 KiB) Viewed 9411 times

Screenshot 2025-03-03 at 12.02.40 PM.png (62.37 KiB) Viewed 9411 times

[DrJJWMac]

I am responding to your second question about exporting the notes. In addition to the Extract Notes and PDF Annotations option, I've cobbled together a workflow to export information from Bookends to Obsidian.

https://forum.obsidian.md/t/workflow-ex ... dian/57867

Someone may have a suggestion to export information to Devonthink.

[SarahG236]

Thank you! I do indeed use Devonthink (and I'm a bit of a luddite with it, so hopefully someone has something straightforward )

[Jon]

There is the option to export Reference Notes and/or PDF Notes. What other notes do you have that you want to export?

Jon
Sonny Software

[SarahG236]

I actually think I can already do what I need to do, I just hadn't found the File menu item to Extract PDF notes and annotations until your first message. I was looking in the PDF gear wheel menu that only lists Export PDF with or without notes, and I didn't want to export the PDF as well - maybe that Extract option could be added to that menu so they are together?

I also think I have worked out the issue with the absent annotations and notes, and it's me not understanding some of the terminology in Bookends:

I didn't understand that "Notes" (in whatever the name of the reference pane is where you can switch between Main, Notes, and Attachments) is referring to a different kind of notes from the ones in the notes stream. I imagine it's only me who has ever had this issue, but I would have found a clearer distinction between those two kinds of notes helpful, like maybe "Memos" instead of "Notes" in that reference pane, or "Annotations stream", or calling the post its "Comments"? I'm also still a bit unclear on the difference between a "note" and a "PDF note" when you click on highlighted text and have those options to add things.

Anyway, thank you for your patience while I figured that out!

Sarah

[Jon]

"Notes" (sometimes referred to as "reference notes") usually refers to the data stored in the database. Just like authors, titles, etc. It's text for a reference you have entered from the keyboard or imported.

We use the term "PDF Notes" to indicate note annotations you have made in the PDF. They belong to the PDF, not Bookends (they are not in the Bookends database).

BOTH can appear in the notes stream as notecards The former can be edited (they are in the database). The latter can be edited if they are PDF notes, but if they are highlights they cannot be (hence the lock icon).

BOTH can be extracted, and the configuration dialog makes clear the difference (Reference Notes vs PDF Notes)

Having different kinds of notes can be a bit confusing, but in general they are labeled as to which are which in the UI.

Jon
Sonny Software

[msteffens]

Someone may have a suggestion to export information to Devonthink.

W.r.t. extracting annotations from a PDF and directly importing them into DEVONthink, have a look e.g. at the recent "Exporting annotations?" thread in the DEVONthink forums, and see also the scripts linked in that thread.

[SarahG236]

Thank you very much!

[c.callicott]

I'm having this problem also. The user manual makes it sound like highlighted text from an attached PDF should appear in the notes pane and notes stream--correct? The annotations I've made using Skim aren't showing up--perhaps understandable, though it would be very nice if they did--but neither are the highlights I've made in the "attachments" pane of Bookends' own edit window.

Second question: How do I open an attachment/pdf in a separate display pane using Bookends' native or preferred software? The User guide says, "Although you will usually view and edit PDF attachments in a dedicated display pane, you can also do so in the edit pane Attachment tab." I can only seem to view them in the edit pane Attachment tab. If I right click in the finder and choose Open with > Bookends, it takes me through the reference attachment dialogue and doesn't actually open a PDF for me. I can right click on a reference in the Bookends library window list and ask to "open attachment with >" but I don't know which of the several unfamiliar or familiar software choices is the best one to use, for getting annotations to show up in the notes stream. I prefer skim, but that doesn't seem to play well with Bookends.

[Jon]

Check in the PDF settings (click on gear action menu in the PDF viewer) and make sure that option to show highlights in the note stream is checked. As for Skim, it uses it's own proprietary method for handling highlights and notes, which can't be read by other PDF readers (try Preview, for example). If you export, you have the option to to save the "embedded notes", which Bookends and other apps can read. I don't know if there are other ways to do that without exporting.

The usual way to view PDFs in Bookends is in the PDF display pane, which by default is below the list of references. There are many ways to open it, but the most obvious is to click on the paper clip icon at the bottom of the library window.

Finally, Bookends reads and manipulates PDFs attached to references in your library, not random PDFs on your computer. When the Finder sends a PDF path and an "open" event to Bookends, Bookends will offer to import (attach) the PDF, after which you can view and/or edit it. The ability to import PDFs and often its metadata with a right-click in the Finder is a feature, not a bug.

Jon
Sonny Software

[c.callicott]

Hi Jon,

Thanks for this info and for getting back to me so quickly. Yes, the settings are correct for showing annotations in the notes stream--that was the first thing I checked, and I meant to mention it in my post. I just went back to look again, and I unclicked and then re-clicked that setting, and now they're showing up. So maybe that's a tip for future users.

A new question arises though: The article page numbers are 269-283. The article has a JSTOR cover page though, so a highlight on the first page (p. 269) is named @270 in the note stream annotation. I saw a place during import to list a first page, but how do I fix it post-import or post-attachment?

Thanks,
Christina

[Jon]

You can open the PDF in Preview (or probably Skim or other PDF readers) and delete the cover page.

If you have imported the annotation and page number to Notes, you can also edit the notecard by double clicking on it to set the page number.

Jon
Sonny Software

[c.callicott]

Ok thanks Jon.