Zotero 6 Annotations

Questions & Help
1

Hi,
I have been using Zotero 6 for reference management and annotation (since with v6 there is a pdf reader). I use “Add Note from Annotations” in Zotero to create an “Annotations” Note:

image

However when I use “/Zotero” to load the reference and its annotations to Logseq, there are 2 problems:

  1. The links to highlights are lost. (Clicking a highlight doesn’t open up the section in Zotero PDF reader) → workaround: Zotero 6 Annotations - #2 by nottakumasato

  2. All annotations are in the same block so it is impossible to refer to a specific highlight: → workaround: Zotero 6 Annotations - #3 by nottakumasato

    image
    image2170×1519 347 KB

  3. Area highlights show up as italic “image” when copy-pasted from annotations note export: → workaround: Zotero 6 Annotations - #4 by nottakumasato
    image

Is there any way to fix these issues? Or any workaround for the time being?

Thanks in advance!

Setup:
OS: Windows 10 Desktop
Zotero: 6.0.10
Logseq: 0.7.8

2 Likes
2
  1. The links to highlights are lost. (Clicking a highlight doesn’t open up the section in Zotero PDF reader)

I found a workaround for this: Right click on “Annotations” note and click “Export Note…” and save it with Format=Markdown & Options with Include Zotero Links checked. Then if you copy-paste the markdown in the resulting file to logseq, then the zotero links work

3

All annotations are in the same block so it is impossible to refer to a specific highlight

Workaround for this was to copy-paste the Annotations.md (from Zotero) without the first two lines:

# Annotations  
(7/26/2022, 4:17:43 PM)

which resulted in:

image
image2124×440 64.2 KB

4

Area highlights show up as italic “image” when copy-pasted from annotations note export:

Workaround for this was to manually use the snipping tool to replicate the area highlight and paste it into logseq and deleting \[image\]:

image
image1668×1457 190 KB

5

seems like we need a plugin to automate these formatting tasks and save the notes file directly into logseq’s library

9 Likes
6

The other functionality would be to update/sync new highlights and annotations made in Zotero (or any other reader) to the Logseq page. At the moment, I have to delete the page and import it again to capture new highlights.

I envisage an “sync” button under the Attachments block

3 Likes
7

I just noticed something funny about this “Add note from annotation” in Zotero.

Scenario 1: If I open the note in Zotero and copy/paste all of it (including the “Annotations (date)” then the links work in LogSeq, but they are all in one block.

Scenario 2: If I don’t select the “Annotations(date)” then the links do not work in LogSeq

If I select all the annotations without the first two lines inside Zotero (not exporting as markdown), then paste it into Notepad before going to LogSeq, the links show up. and I can copy from notepad into LogSeq and everything works fine!!

I can see in my clipboard that the links are being copied with the annotations from Zotero, but for some reason, LogSeq does not like things being copied from Zotero, but it does not mind the same thing from notepad!!! which is so weird!!!

tl;dr: you can skip exporting into annotations.md file if you keep Notepad open and paste it there before going into LogSeq.

8

I think I have found a workaround that I’m satisfied with.

  1. In Zotero, go to Preferences>Advanced>Config Editor
  2. After accepting the risk, search for “Annotation” and change the following values
  • extensions.zotero.annotations.noteTemplates.highlight → <ul><li>{{highlight}} {{comment}}</li></ul>
  • extensions.zotero.annotations.noteTemplates.note → <ul><li>{{comment}}</li></ul>

You are essentially modifying Zotero to create the bullet points for you, but you need to do this formatting in HTML which will then be converted to markdown internally.

You can go to Preferences>Export and change the Note Format to Markdown in Zotero to always have markdown output, this way you do not need to export into markdown and create unnecessary files.