How to extract taken notes for writing new article?

Until now what I have come across is how can we use Obsidian to take notes.

I would like to know has anyone use the App to outline new ideas and writing articles based on taken notes?

I read an interesting article recently; Visualize Connections between Your Notes with Roam Research and InfraNodus

Can we extract taken notes to a “new note” based on what I am interested in from the “Graph View”?
For example, let’s take first map of that article;

In Obsidian is there a way that I could extract these linked notes (i.e. Yellow and Green) to a new note from the database?

A similar type of question floating in the forum, however, I don’t see many practical responses from the community. So thought to ask by myself too.

Or still, this kind of Roam features not available in Obsidian?

Would like to hear from @santi @akaalias @matthewhirschey @tallguyjenks ; if you have found any tips (Tagging you guys based on Obsidian activity - apologies if you are disturbed)


Hey @Bioworld awesome question!

The first part of the process in my opinion is to get familiar with the concept of Zettelkasten, the key is to develop a system of highly interconnected notes, that are design for later discovery and elaboration of creative output (such as an article, essay, book)

Here’s my Zettelkasten example:

To be honest this is a question I’ve been dealing with for a long time now. This is one of the key things I’m planning to teach as part of the system I’m creating for my My Obsidian Online Course and plan to demo in my YouTube channel.

I havn’t made my system fully public yet, but feel free to message me if you want to get updates once I put together content on how to do it according to my system.

While I keep getting my process ready, feel free message me if you want to learn more about my system


When you say extract taken notes, you mean to select them in the graph view? perhaps a select-paste mechanism into a new note could be useful. The new note can show the contents with ![[transclusion]]

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Hi Cristian. Thanks for the reply.

I mean, for an e.g. based on above Figure;
Let’s suppose I can visualize the main distinct networks in our taken notes (broader topic) and I can think there is a clear gap/s that we can answer in a new essay.

So these networked notes are scattered in different notes (.md files) in my vault.

To write a new essay to represent these network ideas, I want to bring them into a new single .md file.

Yes, I agree select paste method would work. But how can I know based on what tags, above network, was created? I mean is that one tag? or several tags? I believe to do this we have to manually find the tags? can not use the network map, am I correct?

Also, what do you mean by ![[transclusion]] (Sorry I am not an IT pro :upside_down_face:)

Thank you Santi. Great stuff. Surely keep me updated once you release the course.

I feel I can easily take notes on OneNote / Excel; however what more fascinating in this network analysis and using taken notes to create new ideas. Therefore I am interested in learning Obsidian.

I am particularly interested on this very topic.

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Like @cristian mentioned ![[transclusion]] are the way to go. @Bioworld The word “transclusion” is really confusing specially considering it’s basically a made up word in the PKM (Personal Knowledge Managment) world.

It basically consists on emebedding the content of the notes in another note.

Actually, in my system for writing articles, this technique of ![[embedding notes]] is something I’ll cover in detail in my Obsidian Online Course, I know that it’s not a very intuitive concept to understand, so I’m breaking it down a lot to make it fully understandable, since it’s such a powerful feature.


Hi Cristian,

Was googling what you have mentioned. That is interesting and seems I can grasp what you are mentioning.

By any chance would you be able to link me to any available example (is there any demo vault in GitHub or somewhere I could refer and understand this concept)?

I came across another resource by @microbit Real Bi-Directional links and Graph extraction from paragraph link co-occurrence

If I understood correctly, this is something similar to what I am looking for. isn’t it?

For an e.g. let’s say I am interested in writing about “Regularization” based on my map.

So what tools should I used to create a new note to embed these notes. Are these based on Tags? Backlinks?

Sorry, I am not a very tech person. Trying to understand the concept behind the Obsidian for writing. Would be grateful if you could help me finding a resourceful example if possible.

hi @Bioworld

To understand embedding notes is better is to experiment with it.

According to the example, you could do it in the ‘regularization’ note. You can open write and preview modes simultaneously to make it clearer. (ctrl-click on the note icon top right).

Then add some interest links using the usual [[link]] notation plus a ‘!’ sign that tells obsidian to embed the notes’ contents in the preview mode.



Embedding notes allow you to build a ‘linear’ document in the ‘regularization’ note. For me, this approach is useful only sometimes,


I have to say that I don’t have a clear idea or workflow of how to ‘write articles’ using obsidian. For me, it depends on who is going to read it.

To relate and choose the order of the topics is an essential part of the writing process. I usually rely on pen and paper and occasionally on other tools specifically made to write, like But this means to repeat the content in several places, which I don’t like.

in short,
I’m also always trying to figure out better ways to write, :slight_smile:

I can imagine an integrated tool that works side-by-side with obsidian, but I haven’t found it yet. Perhaps it would be cool to develop it.

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Thank you Cristian.

This is for academic purposes, for the university.

I am not going to use Obsidian as a tool for writing.

I only want to use this as a note-taking and networking tool to assimilate literature notes to generate new ideas, identify gaps in the knowledge. And extract into one doc with these embedded notes.

Then, MsWords and Mendeley is the best for downstream writing purposes.

I am curious to use Obsidian to identify knowledge gaps, relationships. Thanks a heap.

This is a fascinating area I’m also curious about.

At the beginning of this thread, you added a screenshot of ‘Infranodus.’ I’ve only seen videos of it, but it seems to work at the scale of words. On the other hand, Obsidian works with notes, a different scale.

I miss something that let me work on an adequate scale to write a paper. To talk about a problem, express a rationale, lay an argument network, etc. There are also important space constraints, summarization is important there.

Perhaps in the #academia channel in discord, you can gather more ideas about this.

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Thank you, Cristian. Very kind of you. Please update the thread when you come across new info RE this, I will do the same. Cheers!

Hi Everyone,

Someone was kind enough to point me to this great question on the forum and asked me to comment. I had success in getting a peer-reviewed research article accepted for publication at the top journal in my field by mostly using Obsidian! It helped me to take what should have been a multi year research to just a few months. You can learn more about the research aspect of it here:

As far as the drafting part, I wasn’t able to elaborate too much so I will provide some of my thoughts here. Feel free to ask any follow up questions!

Drafting was one of the best parts of Obsidian. My article, which is about 13k words, has 105 notes and many articles, chapters, monographs, etc. from a wide range of disciplines. At times it was very overwhelming.

For me personally, I never found some of the features of Obsidian and even Roam practically useful (e.g., the visual graph). The features were impressive certainly, but it didn’t actually add direct value to my research/writing process. (Feel free to offer suggestions, however; I’m probably under-utilizing Obsidian!)

So the way I used Obsidian was more like a tool. The flow of drafting/writing was still the traditional way:

  1. Make a list of key points that I think are original to scholarship
  2. Organize those key points in a way that is logical and that flows within existing scholarly discourses
  3. Organize these same points (and I probably need to add a few points) in a way where it can look like a research article. This is the tentative outline that I will begin with.

I do all of this with multiple panes in Obsidian so that I can write my outlines and lists while still being able to access my notes, etc. If I have been able to write good notes (see video on what I mean by that: helpful abstracts, linking to other ideas along the way, etc.), then I should be able to fill each one of the points in my outline/list with the notes on various articles, chapters, monographs, etc. And in those notes, I should also have links to other potentially relevant ideas.

Then all of a sudden, I have a robust outline of my paper with each outline item filled with the literature that I will most likely have to quote/cite.

Then I begin to write my draft, which is basically an iteration of what I’ve mentioned above. That is, each outline item is further divided into its own outline (but now the outline items here are sections and then subsections and then eventually paragraphs). So in the end, I’m atomizing my overall argument into sections, into subsections, into paragraphs, and ultimately into sentences. And at every step, I have all of my notes that are succinctly summarized with salient points and with links to other relevant literature to make it easier for citations.


Last week I processed research notes I wrote ten years ago using another notebook (ZIM).

The graph view proved to be a valuable tool to recall ‘what was there’ and to ‘plan how to connect’ these notes. It helped me to do some synthesis.

The graph has many opportunities to improve, supplying more insight and allowing to manipulate notes. Perhaps it evolves into an even better tool for thinking in the future.


Thanks Jason! I watched the video some days ago, but you are right: this important part of the practical work was missing. These explanations make the process clearer.


Hi Santi, Do you have an updated workflow for this, an article, or a Youtube video?
Or does your course cover this topic?