Hey georgie, had the same problem. Your citation/bibliography style must be the same as your Quick Copy item format in Zotero (Preferences > Export > Item Format).
If not present, you can add new styles under Preference > Cite > click ‘Get additional styles’.
Are you by any chance using IEEE with URL in Obsidian? If so, the regular IEEE format in Zotero won’t work; you’ll need to actually add ‘IEEE (with URL)’ as a style.
Hope this solves your problem!
Thanks for your help, tidebo, I checked and I do have the same style in the quick copy item format in Zotero and in obsidian, and after double checking and trying the import again I still get the same error message. I’m not using IEEE with url as far as I know - what is it?
Is there anything else I could have not set up properly?
Really like this setup - however - if I copy your exact template - all my annotation callout boxes have the same background color. Do you know how I can fix this?
Man you did such a great job! Your Idea with Colored Callouts is outstanding.
Thanks a lot! 
Thanks for posting! I have a problem and am interested in help on figuring out. When I read articles my red highlight means never read this again. Saves me from reviewing impertenant portions of articles in the future. But I don’t want these brought over to my Obsidian vault.
Is there any way to import annotations without importing the red color highlights?
Thanks!
Have you the CSS snippet option turned on ? Or do you have the css file on the right folder ?
Like @odulhin mentioned, you might have forgotten the CSS snippet.
Alternatively, just on the off chance you or someone else runs into the same niche issue as I did: if you “Add a new note from annotations” in Zotero, the imported annotations won’t show up in call-out boxes at all. They’ll just look like plain text. The Zotero Integration and this template draw from the annotations themselves, so if you’ve got an Annotations note attached to the ref you’re trying to import, you can probably delete it.
If you do that and then find that no annotations are imported at all, check how many PDFs you have attached to the reference in Zotero. As far as I can tell this template only draws annotations from the top one, so delete any duplicate PDFs until your annotated PDF is the only one remaining. Those two steps fixed it for me.
I would be interested in seeing a template that could pull annotations from multiple PDFs, since having duplicates appears to be a relatively common problem for me.
Hi to be honest with I struggled quite a bit to write my template but I found a post which seems to answer your question Zotero Integration – Import Templates? - #133 by jujumartini
Hi, thanks you very much for the template. I have a question : is there a way to change the color of the highlight ? I find it very bright and i wanted to get the citation without it.
thanks for your help!
Thanks to everyone on this thread who has been so generous with their templates/responses. As a complete Obsidian newby, with limited scripting skills (very limited), this has all been extremely helpful.
@nocona I have managed to implement your template, and in doing so have a) learnt a fair bit about obsidian, and b) found a solution that suits my use case and level of skill. Thanks again.
How can I activate the CSS snippet? Can someone help?
My final template with Tags imports included. thanks to @Albialy
---
year: {{date | format ("YYYY")}}
tags: research, {{allTags}}
authors: {{authors}}
Abstract: {{abstractNote}}
---
### {{title}}
{{pdfZoteroLink}}
### Notes
{% for annotation in annotations -%}{%- if annotation.annotatedText -%}{% if 'Red' in annotation.colorCategory %}
##### {{annotation.annotatedText | escape }}{% else %}
<mark class="customZot-{% if annotation.color %}{{annotation.colorCategory}} {% endif %}">{{annotation.annotatedText | escape }}</mark> ([{{annotation.page}}](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.page}}&annotation={{annotation.id}}))
{% endif %}{%- endif %} {% if annotation.imageRelativePath %} ![[{{annotation.imageRelativePath}}]]{% endif %}{% if annotation.comment %}
>{{annotation.comment}}
{% endif %}{% endfor -%}
Hello, please could you help me! I’ve been trying to use this template and thought I’d set it up correctly but for some reason when I import a paper from Zotero using the template only the annotations are imported but none of the tabs or bibliographical information. Could you advise where I am going wrong? Thanks in advance!!!
Just wanted to say thank you for this. It works really well for my workflow.
Hi, thanks for this really useful template. I’m having trouble with the bibliography: it keeps appearing two lines below the {{bibliography}} marking. I’ve got zotero integration extension and Zotero export style both set to Nature.
This section of the template looks like:
**Citation**:: {{bibliography}}
but I get, for example
Anyone know a solution to this? Thanks!
Numbered bibliography styles have line breaks in them. You can correct this by replacing line breaks with spaces. This should do the trick (it’s what I do in my template):
{% if bibliography %}**Citation**:: {{bibliography|replace("\n","" )}}{% endif %}
Annotations already have a default URI, I really have no idea why anyone would use the following:
zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.page}}&annotation={{annotation.id}}
This is not only unnecessarily complicated, but it will also fail automatically if sources are not located in “My Library”, e.g., group libraries. Exchange it for the following:
{{annotation.desktopURI}}
