I am also a researcher. For now, I use the following route.
In Zotero beta.6:
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while reading an article in the Zotero PDF reader, I highlight the text I’m interested in, and annotate it, usually linked to the text I’ve highlighted. I always separate the highlighted and annotated texts by color, according to the topic I’m interested in.
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When I finish with the article, in the left panel I select the different colors (each one associated with a particular topic of the article).
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In the right panel, I create a new note (with the option “Add item note”). First, I give a title, which will be the name of the note that will group the annotations of a given color.
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I move the annotations of the selected color (in the left pane), to the newly created note in the right pane. Of course, I have a template created for those notes, so that they will be formatted the way I want when I export them to Obsidian.
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I repeat steps 2 to 4 successively for each color (each color associated with a topic).
At the end, I have a group of notes associated with each article, with its own title.
In Obsidian:
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I create an MD note with the “Citation” plugin, for the article I worked on in Zotero.
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I drag-and-drop each Zotero note, to the Obsidian MD note created in step 1. By doing so, each note brings its own title with the topic I had assigned to it in Zotero, as well as the backlinks to the Item in Zotero and to the PDF directly.
I hope it can help you…