How do you read & process material

How exactly did you export your notes from Instapaper in markdown? I don’t see an export option :thinking:

In the app, At the bottom of an article, I select “Share All Notes” and choose Markdown.

I just checked, and this feature isn’t in the web app.

Thanks for the tip!!

Thanks all for the post. Really great to read all tips. I am also new to Obsidian but getting deeper into it.

I got the same challange as author so I wanted to share how I do it.

  1. Kindle highlights - up to date it was via Readwise - but I have switched to Obsidian plugin and it is the same, so I have resigned from Readwise.

  2. Articles - here on Macbook I use MarkDownload - Safari extension
    on iOS - I switched to Matter - as reading app - and overall experience is just superior + plugin with Obsidian for automatic synch

  3. Twitter - I use Obsidian plugin - and here Readwise was much easier - but I treat Twitter as last thing I want to keep.

I’m new to Obsidian (but not to personal knowledge management), so I’ve been thinking a lot about this too. The beauty of Obsidian is the flexibility, but it’s also what makes it hard to get your head around!

I’ll share my use case, in case it helps anyone’s thinking. FYI I’m on MacOS/iOS via iCloud/GDrive/DropBox for all my workflows.

The problem I’m trying to solve is how to better utilise my paper and digital notes as ‘scaffolding’ for my thinking/learning process, whilst I make sense of and digest new ideas and information. I also want to collect and organise my thoughts and ideas, for use in projects.

So I want to use Obsidian:

  • to re-discover notes I’ve written and forgotten about
  • to show me notes relevant to what I’m thinking about
  • as a place to ‘park’ ideas and thoughts.

I mention this, because for me I’m not looking to use Obsidian for file management. I use DevonThink for that. And I take notes in lots of places that naturally fit my workflows and personal preferences/habits, so I don’t want to force-fit everything into one workflow (I’ve tried many times in the past, and failed).

I plan to migrate ALL of my notes based on input from workflows using a combination of apps that I’ve settled on for now, from which I can export useful snippets or entire notes to Obsidian for making connections:

  • Drafts5 - for note taking/creating drafts in markdown format
  • GoodNotes5 - for pdf mark-ups and my digital planner (great hand writing recognition/OCR/markdown export)
  • LiquidText - for ‘collections’ of research papers I’m thinking about, and for its subsequent annotations export (I do the review of paper collections here, and then send my notes and extracts to Obsidian)
  • Concepts app - for mind-mapping/brainstorming (pdf images/text export); Concepts is a vector-based graphics app, so you can zoom in or out and never lose resolution; it also utilises layers, so you can create mind maps with multiple layers, edit your mind maps, cut and paste between them, add layers of comments or revisions, etc… I prefer it to any purpose-made mind mapping app, and it even has an “infinite canvas” for really huge mind maps!
  • Apple Notes - for journal notes (now migrating to Obsidian)
  • Notion - for project organisation (now migrating my notes/ideas log)
  • DevonThink - for filing the output from all these apps, plus original pdf papers, and paper MindMap scans, and for its metadata and powerful search.

So the file structure I’m testing at the moment looks like this:
Image 07-01-2022 at 15.46

My logic is a bit different from the topic-/category-based folder structure, since that it taken care of in DevonThink. The folders are organised around my ideation flow, not formal disciplines and topic/keywords (I use tags for that). 95% of my notes are in the two TIP sub-folders ‘Notes’ and ‘Journals’ and so the other folders are for index-style notes only - so I may decide to drop these later if I find I’m not using them as planned. Roughly, this is how I’m trying to work:

00 - Filing

Exported extracts and Drafts5 notes are sent here, unless I create a new note directly. I can also send files from DevonThink here, if I plan to create a summarisation note around them (first readings and annotations are always done in other apps above that have better UI for that task).

10 - TIP

TIP is my shorthand for “Thinking in Progress”. I am borrowing here from Malcolm Gladwell’s Masterclass (on their .com site if you’re interested) on his writing insights. Gladwell made a simple distinction between “Thinking” and “Talking” that really helped me, so I’ll share it here.

Gladwell said that there are are two distinct phases in his ideation as he’s writing: he can either “talk” coherently about something, or he can’t! If he can’t, he’s inevitably still “thinking” about it, and his thoughts are still emerging, confused, a mess even. It’s very hard to “think” out loud and be coherent (especially for introverts, who tend to prefer to process thinking internally before speaking to others), which makes me feel better about my own first drafts! Prof Ken Atchity says something similar: he says you should only sit down to write, when you’ve figured out what you want to say. Which is what I want to use Obsidian for: figuring out what I think and want to say. (search on YouTube on the “Film Courage” channel if interested in Atchity’s ideas).

“Controlling Ideas” is another term I stole from Gladwell, or rather from a story his editor tells about how Gladwell found his voice. Controlling Ideas are the long term topics I’m curious/passionate about, committed deeply to, and which find expression in my work. Here I keep Index-on-steroids-style notes so they are easily found - these controlling ideas notes serve as a sort of ‘mental radar’ to help me prioritise and focus my reading and thinking time. They are the helicopter view of my workflow.

“Deep Dives” are also Index-style notes on things I’m learning (like Obsidian), or problems I’m working on, or chunks of larger projects that I’m collecting information and ideas for. They are more output focused than controlling idea notes, which tend to be learning oriented and longer-term.

“Notes” comprises all my book and pdf ‘long notes’ plus lots of so-called Atomic/Zettelkasten style notes. This is a new aspect of my workflow, but I’m excited about it. I’ll often extract atomic notes (using Notes Composer) from imported notes from Notion, or from a new note as I’m writing it. Or I’ll take extracts or quotes from my learning logs in my journal (after reading a book, say), or from pdf research papers (eg extracts of highlighted text or annotations). For quite a while now, I’ve gotten into the habit of writing “note to self: …” in my note-taking everywhere, when I want to write down my own thoughts and opinions, in order to make these “thoughts” stand out from my other notes. So I have a “note to self” template in Obsidian, and a duplicate template in Drafts5. I also write “Notes to self” in Apple Notes and in my diary… so Obsidian is the perfect place to collect them all.

Finally, “Journal” is where my daily journal notes go, plus my learning logs (based on books, audiobooks, YouTube videos, or daily experiences) and bullet journal style trackers (a new thing I’m experimenting with).

20 - WIP

Here I’m keeping project notes, mostly for reference and inter-linking with TIP notes. I’m not sure yet if I’ll need this long term, as it can overlap with Notion. But the idea is to have a central index-note for each project that makes it easy to find all the documents I need, with links to related notes.

30 - Out

Some notes get turned into content first drafts, or talking points, or other forms of re-hashed notes that are “output” oriented. Again, I’m not sure if I’ll need this long term…

40 - Storage

I keep attachments here, if I don’t want to link to DevonThink files or if I want a duplicate, clean copy of a pdf or image in Obsidian.

Notion Archive

All my imported notes, which are moved into TIP as needed.

In Conclusion

I’m pretty sure I’ll be able to slim the folders down further with some experience. I’m still experimenting with Workspaces and Graphs, and I expect to find some of these folders will prove redundant.

I’m not currently using any community plugins due to my uncertainty/ignorance about the data security/malware risks. So I’m also playing with Mermaid to see if this is a better way to create visual indexes for deep dives or controlling idea topic maps. We’ll see: I tend to prefer creating maps by hand on A3 paper or in the Concepts app on the iPad Pro, but there are no hyperlinks available this way - so that’s something I’m still trying to figure out.


Hello NeuroJitsu,
I’m new to Obsidian and just playing around to see if it could be useful to store excerpts and notes from LiquidText. Could you explain a little more how do you send your notes from LT to Obsidian? I find that LT at present is very cumberstone when it comes to exporting
Thanks a lot, very curious!

Hi @nestorito - if you open a document in LiquidText and click the top right icon for sharing, you’ll get some options. I have used both the PDF File and Notes Outline options under “Export File Other Apps Can Open”.

For simple export of annotations, this works to capture quotes for example, or excerpts of a paper/document for reference within Obsidian. You can simply cut and paste into Obsidian or you can work with these notes in some other Markdown app like Drafts5, or create an automation with Shortcuts.

However, the formatting of these LiquidText exports leaves a lot to be desired: they can look very messy, and if you have large collections of papers in a file the exports can get so long you find it hard to navigate the (after export) linear format… which defeats the object of having created LiquidText documents! So I would only really suggest using exports of this sort for quotations and shorter excerpts that you want to cut and paste into other documents.

Getting your curated understanding and insights out of LiquidText and into Obsidian - in a usable form that supports memory recall and navigation of your thoughts - is a MUCH harder task. I’m thinking about this at the moment for my own workflow. My conclusions so far, is that I will probably stop using LiquidText. Because it’s a walled garden app, with such a unique interface, you just can’t really get your knowledge out of there in a usable form. Also, I find the LiquidText mind maps are hard to navigate once they get larger, with laggy performance and poor resolution when you try to zoom out for a ‘bigger picture’ view. So I’ve found myself using LiquidText less, and going back to mind maps that are hand drawn.

I don’t know about you, but it takes me hours and days (sometimes weeks) of thinking and reading time to process a collection of research papers in LiquidText (or using any other workflow for that matter), so I have started to find it frustrating that I can only really ‘think’ about my reading and notes within LiquidText. If you are prepared to do all your thinking in one app, LiquidText is as good as any I’ve found. But the problem for me is that I then want to generate my own writing about thoughts and ideas, which usually involves mind mapping and drafting/re-drafting text and graphics… and this gets cumbersome once I’ve “processed” my reading in LiquidText and want to work in other apps.

Just my two cents…

My latest workflow that I’m experimenting with is:

  • I export a new pdf collection into GoodNotes for reading and highlighting plus hand written notes in margins: I find the handwriting and highlighting with an Apple Pencil on iPad is enjoyable, and hand-written notes can then be searched (GoodNotes has the best OCR for handwriting recognition of all the apps I’ve used - as good as Evernote)

  • if I want to create a MindMap at any point, I either do that inside of GoodNotes (by adding a new blank page in the relevant document) or by using a graphics app (Concepts5) and then exporting the file as a pdf into DevonThink - GoodNotes has better handwriting recognition for text search, but the advantage of Concepts is that I have more flexibility to go back and amend or add to the MindMap later

  • I export from Goodnotes/Concepts into DevonThink (“PDF + Text” file format): DevonThink has fantastic metadata functionality and search, so I keep all my long form notes here

  • I export annotations from DevonThink that I want “to use” for thinking in Obsidian as a new note, with a link back to the DevonThink file and I embed any mind maps I’ve drawn (PDF file embeds)

  • from here, I can carve out any quotes or annotations into smaller “atomic notes” for further linking if required…

Clearly, this doesn’t replace the LiquidText functionality which is unique. I find that what I do miss about LiquidText is how easy and fast it is to navigate around LiquidText notes, annotations and mind maps in a single document. That is unbeatable. BUT the price you pay is that those notes are forever locked in a walled garden, only really usable in LiquidText. For me, the problem with this is that once my memory of that reading has faded, the LiquidText document becomes less intuitive to find my way around… so for long term reference, I’ve decided I’d rather be using Obsidian and DevonThink.


Hello @NeuroJitsu, I’ve been ‘out’ for a while so sorry for not answering your much detailed description and thanks. To make it simple: here I’m experiencing more or less the same. The main workflow-breaker is, as you say, LT (messy export), even if with the last update with “linking options” something changed. But that’s not the real point to me which is actually to have a reliable export system. Reliable in the sense that I can trust that what is exported is in a clear order (I’m still struggling to understand what comes first and what follows) and that is easily usable in Obsidian that I recently discovered but it seems the real game-changer. Another option could be switching to Marginnote which has a good “bridge” (a MN add-on and a Obsidian Plugin: Obsidian Bridge: About An Obsidian plugin to bridge MarginNote 3 and - Add-on Release - Marginnote). I used MN for a while in the past (and leave because it used to be quite buggy) and so I still have some files with which I could make some experiments…it looks promising. But I like the LT feeling that I’m almost working on paper but with some bonus. So for the moment I’ll try using Goodnotes has my “paper-like” moment in the study process and then put all in Obsidian which is perfect for thinking and memorizing literature. But I hope that a new release of LT will fix the export problem creating a consistent way of visualizing data outside LT itself.
Thanks for sharing!

Hi @nestorito - good luck with GoodNotes experimentation. I’m loving it for markup of individual documents, but as I said it totally lacks the ‘thought navigation’ bit that LT and Obsidian do in their different ways.

One thought I had since, is that in reality all the “processing” of new ideas in our research work happens in our heads, not in the software tool. The ideas that we can “think with” are only the ideas we can remember (ie stored in active, long term memory) and that we’ve chunked/related to “prior knowledge” (ie that we’ve “processed”). Once knowledge is integrated intuitively as part of “what we know” it is not necessary to be able to “consciously” think with it, other than to express our thoughts in writing or in dialogue.

It seems to me, therefore, that the practical question is, “for how long do we need to process new information?”

For an academic or an author, studying and writing in fields of knowledge for a whole career, the answer is a lifetime. Their PKM system, with its requirement to precisely quote sources, is probably the most demanding type. But for most other people, we can really over-think this stuff!

As I continue to develop my own PKM “extended cognition” system, I am trying to keep it as simple as possible. Whilst the documentation of sources is necessary to quote from and attribute to my sources, my atomic notes have a limited useful life.

This ‘half-life’ might be a month, or 6 months, depending on the project. Beyond that, I’m unlikely to refer to them since my “thinking” will have evolved. So I pan to archive notes after a certain half-life (in DevonThink, which has the best search as I’ve mentioned).

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For articles what i generally do is this:

  • skim the article to see if anything jumps out at me
  • if something does, i use the MarkDownload extension to download the article and any articles that get referenced/linked
  • clean up the links so that they point to the .md files in stead of the URLs
  • copy and paste the paragraph that jumped out at me into its own note, which i link to the full article note.
  • tag the paragraph note with any relevant key words, as well as make bi-directional links to any relevant long form notes on topics/ideas i’m exploring.

the only books i generally read, that aren’t one of the 66 in the Bible, are non-fiction so for those i just take notes as i’m reading the way i would for any text book.

I wrote up my current practices w.r.t. note making after/during reading “I’ve read something, so then what?” My Note Making Flow – Interdependent Thoughts