Extract Annotations by Color

chriseu

Hi All,

Zotero 6 is no longer compatible with the Zotfile feature to extract annotations but added the native "Add Note from Annotations" feature. Zotfile was able to extract annotations by color such that different color annotations were extracted into separate notes in each of which only the same color annotations were added. The Zotero 6 extraction feature does not have this option.

Originally, the Zotfile creators understood that it "Would be useful for someone using a color system to categorize his/her annotations, e.g. red = most important, yellow = important, green = background info..." (2014)

Is the above correct that there is no such color sorting feature in Zotero 6? If so, please include this very important feature. Or am I overlooking something? If so, please let me know how to enable it.

Thank you,
Chris

martynas_b

You can filter annotations by color in the annotations sidebar. To select all filtered annotations, use Cmd/Ctrl + A. Then, right-click and choose 'Add to Note' from the menu. Make sure a note is open in the right-hand pane before doing this.

chriseu

Hi,

Thanks so much for this reply. Although it would be better to have an in-built extraction function into separate notes by annotation color, this sounds like a workaround I could do until we have this function.

But I can't get this to work, unfortunately. Where is the setting to filter annotations by color in the annotations sidebar? I created an "Annotations" note from my PDF with the "Add Note from Annotations" function. I have the different colored highlights in the note. But I see no filter settings. I can toggle between "Hide/Show Annotation Colors" only (and Hide/Show Citations, and text formatting options, but those are irrelevant to this issue).

How can I find the filter by color option?

Thank you,
Chris

mjthoraval

The Annotations Sidebar is on the left of the PDF Reader. You can toggle it from the left icon of the top toolbar if it is closed.
You can see the colors and the tags at the bottom of the Annotations Sidebar.
You can click on the colored squares to filter by color, in the same way as for tags in your library.

I haven't tested recently, but you could also have a look at the Better Notes plugin for more complex Note Templates:
https://github.com/windingwind/zotero-better-notes/discussions/227

chriseu

Hi,

Thank you so much I have found exactly what you're referring to in the Annotation Sidebar. I can filter by color and I can select my notes either individually or all of them by Ctrl+A. However, right clicking for available actions, none of the actions actually work. Nothing works either for individual notes or when all selected. So "Add to Note," "Edit Highlighted Text," "Edit Page Number," "Delete," nothing works.

Am I correct in suspecting that this nonfunction is somehow related to the little lock icon that appears at the top right corner of all my notes? I am suspecting that my notes are locked for editing. Is there a way to remove that lock? I have created all my notes in PDF Expert on the iPad. These notes are never locked though in other PDF software I use, such as Adobe, Wondershare and Foxit. In those apps I can freely edit the annotations, including deleting them, changing text, etc. So I wonder why Zotero would be different in this regard.

For testing, I also created some highlights using the Zotero in-built highlighter to check the above functionality. To my surprise, the "Add to Note" function is grayed out and cannot be used even on these notes! I totally do not understand why this is so in case of the in-built highlight. There is no lock icon on these notes, and I tried this test in multiple PDFs with the same result.

So even if I could unlock my notes (how can I do that?), it seems I could still not create new notes from them with "Add to Note." That's a bummer. Am I overlooking something here?

Thank you,
Chris

p.s., I installed the Better Notes addon, but I could not get it to work to sort notes by color, unfortunately.

mjthoraval

To my surprise, the "Add to Note" function is grayed out

You need to open a note in the Notes pane on the right-hand side of your PDF first.

You cannot edit an annotation made in an external PDF reader. But you should still be able to add it to a note if the note is opened in the Notes pane.

To import the annotations made in an external PDF reader to Zotero annotations:

External annotations are read-only by default — indicated by a lock icon — but you can transfer them into Zotero by selecting File → “Import Annotations…” from within the PDF reader, after which they'll be fully editable.

https://www.zotero.org/support/kb/annotations_in_database#interacting_with_embedded_annotations

More information in these 2 pages:
https://www.zotero.org/support/pdf_reader
https://www.zotero.org/support/kb/annotations_in_database

chriseu

Hi again,

Thank you so much, following everything you said, I am now able to create the notes by color as I wanted to. Thank you!

The only improvement that would make the life of folks like me who color code their PDF easier at this point is to automate this manual process by having an option when using "Add Note from Annotations" to add new notes by color.

At any rate, I love Zotero. And I'm looking forward to the alpha release of Zotero 7! (Hopefully, including this feature :)

Thank you,
Chris

adamsmith

The only improvement that would make the life of folks like me who color code their PDF easier at this point is to automate this manual process by having an option when using "Add Note from Annotations" to add new notes by color.

You're not the first one asking -- this would definitely help with larger scale 'coding' endeavors using colors as themes. I think last time devs said they'd consider this, not sure of the current status.

FeralFlora

If anyone here uses Obsidian as their note-taking app, you can use the Zotero Integration or Zotlit plugins to easily extract your annotations to markdown notes, grouped and formatted according to the annotation color. There's a thread in the Obsidian forum showcasing many examples of templates that format the resulting notes according to color: https://forum.obsidian.md/t/zotero-integration-import-templates/36310

Levlin

I just wanted to add that I am also interested in this feature native in zotero :)