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Zotero/etc. and annotations integration

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I am using Zotero's function to extract annotations from Pdfs and would like to import it into NVivo. While NVivo can import extracted annotations in form of memos, there is the problem that the HTML code Zotero uses in order to store the extracted annotations is imported in NVivo as plain text and therefore basically useless for further analysis in NVivo. While copying and pasting the text resolves the problem, it prevents the automatized treatment of hundreds of annotated PDfs. As far as I have tested it, this is not specific to Zotero, but applies to any other reference management software as well.

I attach a screenshot of how NVivo imports the HTML code as plain text (left side) and how it should look like (right side) (I copied and pasted that annotation manually).

As is shown on the left hand side, NVivo translates the HTML code into plain text.


In order to automatize and streamline the research process from the very beginning (while skimming and annotating Pdfs) and automatize it, it would be great to not run into formatting problems further down…


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Hello Patric,

I am not sure what would developers can do to fix this issue

However, as a veteran Zotero user,  I can suggest a solution for a streamlined research process.

Here is what I have been doing since Nvivo's Zotero integration:

Once you begin collecting articles for your literature review do NOT annotate them within Zotero.

This way will help you saving a significant amount of time, since you would not need to annotate and then code your data.

All you need to do is importing a satisfactory amount of articles into Zotero and export them.

While importing references into Nvivo, it is important to select name by author and year so that you can utilize framework matrices for your literature review.

Start reading and coding your articles, once you finished coding you can create a framework matrix to display what scholars said about a certain topic (i.e. node).

What you see on a framework matrix makes your literature review writing really simple. 

Please feel free to reach if you need further assistance about this strategy.

Hope this helps,





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  • 3 months later...

Hi Canarik,

Thanks for your reply. Unfortunately, I have not checked back if somebody answered my question!

Your solution would indeed resolve the problem. However, coding in NVivo is not my preferred way of reading and annotating, although the graphical user experience and Pdf handling has improved quite a bit.

Let's see what the future holds…

Thanks again for your answer!

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