Zotero Question


New to Obsidian and linking overall. I just followed the thread on here also watched some vidz with regards to linking and how to use Zotero for pdfs. A few questions I am not understanding;

The pdf documents being copied to Ob is just the highlighted area of the pdf doc and annotations. What it the more practical approach if I want the entire pdf document copied into Ob? Just highlight the entire pdf document for conversion?

If I have a txt / word document store in Zotero I can simply copy the text and paste into Ob. s can be stores in Zotero and linked to Obsidian. I think the obvious answer is just copy the text document into Obsidian and store it in Zotero in the appropriate folder. But I am not aware of any way to link that word doc in Zotero to the text note now in Ob. Any idea on ht to link that back?


use this syntax to embed the file instead

Can you elaborate I am not sure how to do that?

Also that is fir embedding the full pdf? How to also embed the txt file from zotero?


So I copy and paste the txt from the Zotero file then where the txt / docx file is saved in the Zotero directory I choose right click create shortcut. Drag that shortcut into the Ob edit panel where I copied the text. Now when I click on that link in the edit screen the external app opens the text doc in Zotero I can edit it and changes will be saved in Zotero (need to change markdown text manually if that is my goal.) I need to create that shortcut and be sure to copy that to Ob because just embedding the file itself causes Ob to create it’s own copy of the document in the Ob file directory and Zotero will not be updated tat way.

Is there any way to produce all the text from the pdf into markdown or is that an ocr issue?

i use citation plugin to link to pdf files in zotero from obsidian. unfortunaly you can’t embed/show the pdf content inside the notes, but only you can link them properly so (it is going to change if you change things in Zotero or move to a new OS. I really like devs to add such a feature to obsidian but in the meanwhile you can convert pdf files to markdown via pdf to markdown plugin. you can have the books organized in zotero, and when you need them in your vault search for the citation key or what ever you choose. I do this for epub books a while and it is kinda working.

I am not sure about pdf but for txt/doc files you can just save them as ‘.md’ files. While saving them as markdown files make sure that the storage location is inside your Obsidian vault or in a specific folder inside your Obsidian vault.

Perhaps this extension will provide you some relief.

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This is incorrect, you can definitely embed PDFs as Walrux mentioned above:

To convert the pdf to a markdown note you could try pandoc or I believe there is a community plugin that does that (I haven’t used it, so I can’t say exactly how it works).

For this last part, you can use a linked file:

With linked files, Zotero only stores a link to the location of the original file on your computer. Linked files are not synced, nor are they deleted if the attachment item is deleted in Zotero.

how? i would love to do that. i can’t see anything related to that in Walrux posts. I mean it is possible if you use the absolute path in the storage and never change the location of library (like any other file in the storage), but you can’t embed them using a zotero URI as far as I know. I specially looking for embedding them by page with better pdf plugin

pandoc can’t convert pdf to markdown for some reason. it says it converts from less expressive formats to more expressive ones, it converts .md to .pdf but not the other way

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Ah, my bad, then I misunderstood. If your PDF lives outside the vault, indeed it’s not possible to embed it nor is it possible to do so with Zotero URLs.

A workaround would be to use Zotfile to move your PDFs inside your vault, and edit your citations/mdnotes templates to embed them. This is of course a trade-off if you’d preferred your PDFs lived somewhere else.

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In that case the community plugin might be the only choice.


i though a bit about this. it would be easy to embed them if we can give the location of zotero library to obsidian as a variable. i think Rmarkdown does something similar with markdown within notes. but it is going to be in the whole vault/global. also it is not very hard to change the URL of files in batch via regex in case one changes zotero library location. but something like the former solution is better in the long run. Maybe if citation plugin could get the URL of the item on the hard drive i could use it, but right now i can’t convince myself to use these.

yes, it very good in my very limited experience that I had with it. but it is going to be messing in case there is a table or something like that in the file. there is no way around it. I think embedding the pages and copy pasting is a better solution

Clarify? I have two plug-ins added to Zotero - 1) MDnotes for Zotero 2) Zotfile. So with that I highlight certain parts of the pdf file in Zotero then choose the 1) Extract Annotations 2) Export to Markdown. Then the text that gets copied to Ob is whatever was highlighted. These plugins only convert to markdown the highlighted text. Is there another plugin I am not aware of to convert the entire pdf document?

yes i am familiar with zotfile + mdnote workflow and that is great. but you can convert the whole pdf document too with this: GitHub - akaalias/obsidian-extract-pdf: Extract PDFs to Markdown within Obsidian

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Exactly what I need thanks.

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