How to: Reasonable use of links for scientific research

I would like to get some advice from those who are already actively using Zotero and Obsidian for scientific research.
Currently, I make annotations in Zotero and then collectively transfer them to a new note in Obsidian.
From this collection of notes, I create my ideas in the next step, then link them to other notes, later compile them into a first draft, and so on.
Currently, however, I still do it in such a way that I insert the link to the “big” literature note into the short note derived from it and I don’t know now whether that makes sense.
I am a big fan of the graph view and it helps me to discover aspects in the whole again.
How do you do it? Do you use the graph actively?
In my case, a lot of connecting lines are displayed, which only refer from the “big” literature note to the small ones, so that other connections are somewhat lost.
It would also help me a lot if you could give me an insight into your research workflow.
Thanks in advance!

(Yellow represents the “big” literature notes)

Zotero and Obsidian are very good friends when it comes to helping me do research. The most important tool for my worflow is the Zotero Integration extension which allows me to import references and annotations into my vault.

I store one note per reference using a unique key. For instance I have a note called RaspNeuralNetworks2018. This way I have consistent labels for a paper in Obsidian, Latex and Zotero. I use Biblatex to create these unique keys inside Zotero.

When I want to import my annotations, I have a separate Zotero Integration template for that. It’s fairly rare that I import annotations directly. Usually I note down that I read the paper in my daily journal, and I write my synthetic summary in the paper’s note. If I every want to go back to the annotations I use Zotero for that.

As for the graph, I use it rarely and in a limited way, because it becomes difficult to manage after a while (it gets very busy). The one thing that is fun about it is that it shows me areas that are densely connected. So it shows me the main topics I wrote about, and how they relate to each other. But it’s more of a nice thing to look at than a tool for me.

Below you can see my graph. The lower-right part is related to knowledge management, and the lower-left cluster is related to my current research project. Papers are green.

Hope this helps

I’m not in the group you’re asking, but I think it makes sense to keep a connection to the originating literature note.

Also, if you have a way to identify your literature notes (a tag, name convention, folder, etc.) you can filter them out of the graph when you want to.

Many possible solutions and workflows. Here is mine.

(1) Read something in Zotero, highlight things for later processing in Obsidian

(2) Extract annotations from reading and paste into Obsidian (I don’t bother with plug-ins that automate this)

(3) Each quote is it’s own note. Notes are titled using a summary of the quote in my own words, i.e., “X was found to be valid based on Y, suggesting that Z” (these notes follow a basic PEEL writing structure)

(4) The content of these quote notes looks like this:

[[X]] was found to be valid based on [[Y]], suggesting that [[Z]]. Name (Year) used a methodology to arrive at this conclusion. The implications of X are that Z. 

# Sources

* Full APA reference
* Additional sources as I encounter them

You could link to the original note if you want to, but because I include the sources in each literature note, it isn’t necessary for me. My source notes, if I use them, are empty and just serve as something to link to. I’d rather let my literature notes and evergreen notes (original ideas) be linked by concepts rather than sources, but this is a preference and there are valid reasons for linking to sources, such as when doing literature reviews.

(5) Either intentionally or spontaneously, I will combine quick switcher and vault search to create evergreen notes/my own ideas. Sometimes what I think is my own idea is really just a point of departure and I discover that somebody has already studied that idea, which means the line between literature notes and evergreen notes is blurry, but this isn’t a problem because I differentiate them with a simple tag, where a literature note doesn’t have a tag and an original idea has the tag #original-idea

(6) Using a similar workflow to (5), I use these notes in whatever draft I’m working on as they become necessary.

I don’t use the graph, but I do use the Influx and Strange New Worlds plug-ins.

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