Need help integrating JD and my PKM vault in Obsidian


Any Obsidian people here?

I’ve been using Obsidian for my PKM for almost a year. Starting to feel pretty comfortable in my vault. It contains a variety of notes related to life admin, career advancement, projects I’m working on, and just general knowledge and areas of interests.

ACE framework

I use the ACE framework, created by Nick Milo, to organize my vault. If you aren’t familiar, it’s easiest to just share the folder tree:

–Periodic Notes

The problem

That all has been great, but something holding me back has been how I organize my digital life more broadly. In other-words, my once simple folder structure has accrued a certain amount of chaos over many years, as my file management system now spans several devices, hard drives, and cloud storage.

Why I’ve come to Johnny.Decimal

This chaos has led me to the Johnny.Decimal System.

One thing I find really useful about JD is that it is meant to incorporate all aspects of a system or project. Digital and hard copies; cloud or C drive. When set-up thoughtfully, it’s like a filing cabinet that anything can fit in. I can’t really do that with my current PKM in Obsidian.

As I build my system

So I guess there’s some obvious ways to make Obsidian work to my benefit in my system inspired by JD: first and foremost as the Index (00.00 in the system). I’m thinking the index is a separate vault from the PKM I described above. But I’m running into some conceptual issues concerning how to integrate my PKM

I understand Johnny’s stance on this is that your JD system is your Second Brain or PKM system. But I really like how in Obsidian I can link distantly related ideas (notes) to encourage sense making.

So I’m trying to avoid the urge to break up my vault into little pieces. The only way to utilize the functionality of Obsidian is if all of the note files reside in the vault. It can’t access files, say, from a different area or category.

Plus, JD shouldn’t restrict what tools you use.

How you can help

If you have experience with using JD with Obsidian, I’d love to hear how you do so.

Beyond that, I’m curious if you think my current PKM should be considered it’s own system (multiple systems is cautioned against in JD) or if it’s more of an ID within a broader JD system, area and category to be determined.

If anything, please help me avoid splitting up my vault across various areas and categories so I can continue to enjoy the benefits of Obsidian.



Without understanding exactly what your life looks like, I would recommend against making a bunch of separate vaults. I use obsidian and haven’t ran into the philosophical wall of how different notes may link together – in fact – I think it may be a strength
i.e. you are looking for your 2025 financial goals and turns out it’s linked in your 2023 financial report note.
Even better, the linked notes in obsidian can make your index insanely powerful depending on how your approach it.

Hope that makes sense. All in all, I wouldn’t recommend making several vaults, especially since some things will probably live outside of obsidian with an ID attached. That’s where your index comes in super handy.

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That’s really helpful, Ben! Thank you for your input. I totally agree that linking notes in Obsidian can make an index even more powerful if done properly.

I guess I wasn’t thinking about how my current vault basically functions as an index for my life, but without the helpful numbers and in a way that doesn’t allow for referencing things that live outside of the vault. This really peaks my curiosity though.

I imagine my vault becomes my system, and I include an Index note at 00.00 to link all my other AC.ID notes from there. Then I can reference files that live elsewhere using a secondary line in my index note or by creating a note for every ID to collect metadata regarding location.

I need to keep thinking about this. I can see a “Building my JD System in Obsidian” walk-through being a beneficial guide for new users though.

Hi there fellow JD Obsidian traveller.

I am using ACE at the high level. My JD index sits within Atlas/Maps/Home Life Index. Then I use the process discussed here to create the index. Benefit of this, is my final leaf documents can exist anywhere in Obsidian but are still clearly linked.

Hope that helps.

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Ah! Thank you QuantumGardener!

I’ve taken some time to really try to understand the insights you’ve shared.

I also found your post on the forum discussing the very same problem: Using JD in a Digital Garden. It was helpful reading how you worked through this yourself. I’m sure you recognized my struggle, so thank you for reaching out :sweat_smile:

Using the Folder Notes plugin in Obsidian is neat for the index – I’ll check that out. I was thinking of doing something similar to what you did with regards to DV tables to list your index entires.

The distinction you make between knowledge and records is exactly where my problem lies.

Knowledge Records
Created by me Created by others
Date is unimportant Point in time, usually dated
Connected to other knowledge Each record is complete unto itself
Difficult to organise in a hierarchy Easy to organise in a hierarchy

I’m not trying to sort my PKM. I’m trying to integrate my PKM with my record keeping system and my task management system.

Like you mentioned in the forum discussion, this is also a problem of scope. My first scope statement excluded my PKM because I don’t think about my PKM notes with a strong hierarchy in mind. But my PDFs and eBooks like on a hard drive, not in my vault. How do I reference those from my PKM? Or my physical notebooks from college courses? I like the idea of at least being able to reference those with an ID.

My second (current) scope statement starts with “Everything” – we’ll see how that works.

You mentioned that one of the goals for your system was to not split information up any more than you need to. My instincts are the same, especially considering how this leverages the powerful linking features in Obsidian. This also avoids the ‘Multiple Systems’ problem JD points out here.

Main question/concern

More of a concern. I really have to just implement this and try it out. Gall’s law is ringing in my ear informing me to just get on with it.

But something I’m still thinking about after reading your thoughts is just how to implement my Areas and Categories in a way that is compatible with my PKM. Because this extends beyond the issue of PKM now.

Here’s an example. Say I have an ongoing project: A Project. I would usually have an ‘Effort’ note and maybe a few additional notes related to the project. Those can exist hypothetically anywhere in my vault because all that matters is I’ve linked my notes back to the main project note, which appears in my ‘Efforts’ note.

But what if I have a Google Sheet that is related to the project? Now I need to think about what folder in Google I should save that file. Do I make a new project folder? Where area/category does it belong to?

Maybe I’m just looking for clarification on how you reconcile the hierarchy of your JD system with the non-hierarchy of Obsidian, especially when it comes down to the act of choosing your categories and areas.

Something else: does your JD system areas mirror the ACE framework in any way?

I may make an additional post regarding the issue of my scope soon.

I’ve seen people just mirror their JD folder structure in obsidian. So if you’re working on a project, say JD ID 15.02, then all the files would be in a folder structure reflecting that. Inside the obsidian vault there would be a similar folder structure with the notes related to the project in 15.02. In the end I think it’s up to you how you want to do it.

For myself, I’ve got my PKM in a particular JD ID and I don’t bother putting IDs on individual notes.

My JD index is in a vault of its own. However, i feel that defeats the purpose since the point of having the JD index in obsidian was that the JD ID would double up as a note about the project. However, as my system currently stands I have my notes in a separate vault with my index in its own vault. The result is that my index notes are basically empty, defeating the whole purpose.

The more I use the system, the more I’m gravitating away from JD altogether and gravitating more towards simply putting links to all the materials related to a particular ID in the main note for that project.

I realise I may not be very clear. I am half asleep so if anything doesn’t make sense just let me know and I’ll clarify in the morning.

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I don’t know anything about ACE or the other things you mention, but I implemented Johnny Decimal and leverage Obsidian (all in a single vault). For me, the J.D system helps to implement a top-down structure that marries nicely with the bottoms-up network of my ZK in Obsidian. I use a mental model of a library where the “card catalog” is the Index in J.D. There is a folder just dedicated to the catalog in the same vault and I have “cards” which correspond to each J.D ID, Category, and Area. I use the Dataview plugin to help create dynamic tables of all linked notes that tie to the top-down structure and of course I still have the links between notes themselves, though you’d have to navigate across them per usual. This allows me to quickly add a new note and link it to the appropriate card, then the card is dynamically updated showing not only whatever notes I happen to make about the category, but also a nice table of all the notes that link to it along with some properties/metadata of interest. I made a thread on this when I first implemented it here: J.D Organized and Launched!

I still use it and am very happy with it.

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This was my first thought as well for how to make this work for myself. That is, the PKM vault itself is given its own ID within a category within an area. I then started thinking about how the index would look like in this scenario. Would I have a separate vault just acting as the index? Or maybe I make a new folder in my vault named ‘Index’ where I keep the actual index notes?

The second option allows me to link to my index notes from within the vault but also brings with it a host of other questions regarding specific implementation, hence my starting this discussion. You’re right on though.

In regards to the host of other questions, one I’m thinking about right now is whether or not to only create ID cards for things ‘outside my vault’. Not sure if that makes sense to you.

I’ve gone back and forth on this one. Lately I’ve been feeling a single vault solution is the best way to go. This is because the ability to link and tag in Obsidian.

Here I’m mostly talking to myself: Am I really just trying to turn my PKM into a database? Maybe I’m taking the wrong approach to this project. A revisit to my scope is in order.

I’m curious to hear more about what you mean.

Here is a primary source regarding the background of ACE: The Ultimate Folder System: A quixotic journey to ACE - Knowledge management - Obsidian Forum

I like the idea of a “card catalog” for the Index – that’s clever! Also, I’m in agreement on the single vault now. This discussion has clarified things.

Regarding the implementation of top-down structure: it’s un-avoidable. That said, I’m trying my best to avoid it as much as possible :sweat_smile:

I love Obsidian because it allows me to be a ‘middle-out’ processor and evolve my thinking over time. For example, renaming or moving files doesn’t break anything. In fact, it’s almost encouraged in the community. This goes against some aspects of JD, like how it’s not ideal to move an ID once it has its place in the index.

Here’s something else: to me a note (read: thought, idea, thing) can’t be properly categorized by a single folder location. JD solves this by ensuring you create unambiguous areas and categories, meaning that you should know immediately where a file belongs without mistake or confusion. I wholeheartedly agree.

Except that sometimes I want to link a single note several times, allowing myself to categorize that thing several times. Know this is really only the case when I’m talking about my notes related to Knowledge. Earlier, I discussed the distinction between knowledge and records.

In particular, knowledge is difficult to organize in a hierarchy, while records are easily organized into a hierarchy.

But again, structure is unavoidable. Along with categories, classification, and folders. It’s an integral part of learning. These 3-letter PKM acronyms like ACE, MOCs, or LYT help me develop that structure in a way that makes sense to me and evolves with my thinking, without being overbearing or burdensome.

It was really helpful seeing your thoughtful implementation of these concepts in Obsidian. Always rewarding seeing an example of a carefully considered system. I’m glad you’re still happy with your result.

Thank you sharing. I’m finding everyone’s responses very insightful.

I should clarify that you can still use external links to another obsidian vault in a separate index and it will still work. It just won’t show up in a graph view. But if the intent of the index is to be a jumping off point for finding related notes, the external links will work just fine.

My issue is that I’ve got separate systems for project notes, my PKM and JD index. The reason I set it up this way is because I see my PKM as more of a knowledge repository and idea generating machine whereas project notes are more a record-keeping repository. Also a reason for that is because I often need web access to my project notes which obsidian doesn’t offer.

So while I’m not saying JD is useless, but the whole point is for me to find related content. I’ve been doing that with links and backlinks anyway. For example, if I’ve got an email I want to reference, i just save a link to it within a note with the appropriate context. Search utilities today are powerful enough that where there aren’t explicit links I’m still able to find stuff. Because of this reason I have been wondering if JD is just overkill for me and whether it’s just adding an unnecessary layer of friction.

Hope this makes sense.

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I don’t really have any projects at home, but I do use them extensively at work and have spent many years using GTD as my productivity approach.

My immediate thought is the Google Sheet goes into Obsidian as an attachment and is linked to your note. Reason being, that is where you are doing the work.

Area → Category → ID tied to project → Google Sheet tied to project page.

Having said that, I was storing Tax docs in Obsidian, but moved them to Zotero. My Tax id is 34,98 Tax, 2023-2024. The notes are in Obsidian, receipts in a Zotero collection of the same name.

JD index is a hierarchy. The rest of Obsidian isn’t. My website is published using a system called Quartz. It generates from notes in a specific folder. I have notes in my Atlas, then another folder for Quartz (website). All I need to is Ctrl-M (move) and select the Quartz folder to publish. Free from the folder.

Not at all. JD is categorisation. ACE is organisation.

I had to look up Gall’s Law. Had never heard of it. Fair point to be aware of, but I’d caution that perhaps your system does need some complexity to work. The right complexity makes it as simple as possible.

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My take is you are filing so that you can find it quickly. If a note is best in several places, add it to all of them.

At the file level consider using shortcuts.
In Obsidian as I’ve described it, super-easy to add to multiple IDs.
In Zotero you can add a doc to multiple categories.

I have cases of this. Often receipts end up close to the purchase, but may also be tagged for a tax year.

The point is, always aim for a single filing. Take a moment to think where to file. If you genuinely can’t split it, file in all places. Default = single, considered = multiple.

Most systems go astray because we default to multiple.

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If it ain’t broke, don’t fix it.

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Yes it’s always a balance between the top-down (hierarchy) and bottoms-up (network). Although about tagging, I found this blog post interesting relative to the hierarchy/network topic: A Complete Guide to Tagging for Personal Knowledge Management - Forte Labs.

I was missing the top-down aspect in my organizational life which the J.D system helped immensely. Balancing between the two (it’s an ongoing dynamic) and combining in Obsidian brings the power of both.

As to relevance of a note to multiple cards, that’s the beauty of tagging & linking. In a new note I always put the card (the johnny decimal Category.ID card) as I think of it as a property of the note. And then link to other notes in a “Related” section at the bottom of the note. If I think the note is relevant to another card, I simply put that card link in the Related section as well. As implemented, the dataview plugin will pull the same note title/link into whatever cards in the card catalog are linked to the note and regardless of which card (category.ID) in the card catalog (index) I’m looking at, it will appear in the table for that card.

Remember I started both my Zettelcasten and Johnny Decimal system recently, so I’m still a novice to both. But in my reading about ZK, they always talk about a note getting a unique identifier and then later it is organized into an index or lists of content so that it pulls together thoughts (bottoms up) relative to a larger concept. That’s the bottoms up organization that gives the user a way to dive into the ZK rather than just searching. The J.D system for me provides a similar capability. I can easily create a new “card” if needed within the J.D structure if there isn’t one that is a natural fit for something that emerges from the ZK.

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I need some more time wrap my head around all this. I don’t want to rush anything. That said all these responses have been enormously helpful – thank you! Once I finalize the setup my system, I’ll share that. For now, I’ll share some comments on posts I haven’t had a chance to reply back to till.

Good point. I don’t use this feature myself, but I can see how useful it could be for a multi-vault system.

What do you use when not using Obsidian?

I see your point here. I think I feel the same way about my MOCs and dataview tables and just general notes in Obsidian – if I really don’t know where something is, I can always search for it. Google Drive is similar. And Gmail. At a certain point, just use search. However, I recognize the need for some sort of structure. i.e. I’m not the type of Obsidian user that gravitates to folder-less vaults.

I need to more seriously consider how Zotero could be useful to me. I haven’t tried this sort of file database app yet. Maybe it is a part of the solution for me.

Man, I’ve been thinking about this for 4 days straight now and still feel I haven’t cracked the code yet :sweat_smile:

Can you elaborate on this distinction a bit for my sake?

Shortcuts at the file level is a really interesting solution that I haven’t thought about. I wonder if this breaks at some point (thinking about how the shortcuts to my external SSDs break whenever I eject them – not a big deal, but it is a ‘flaw’ in my mind)

This. 100% this. I have this problem.

I am definitely still searching for the right balance between top-down and bottom-up approaches. The Tiago Forte article you mentioned is interesting for many reasons. Thank you for sharing that. I’ve been in PKM for about a year now, this one seems like essential reading.

I appreciate how he questions the widely-held belief that hierarchies are over. He makes the case that not only are hierarchies not going away but that they are actually complimentary to networks. Seeing how he’s come around on tagging is interesting as well. Lots of food for thought there.

How the idea of a ‘Productivity Stack’ plays into this discussion

I brought this up earlier:

It’s not exactly a great question, but I keep thinking about it because I’m still questioning my own ‘Productivity Stack’ i.e. the tools that make up a productivity system. I didn’t realize it was even a term until recently, and I think that’s a part of my problem.

So many people in the PKM community treat their PKM system as their entire productivity stack. That’s cool if you can pull that off, but I’m starting to realize more how my PKM setup in Obsidian is just one aspect of a broader set of systems that I use to optimize my productivity. This article helped to make me more aware of this ‘broader set of systems’: Optimizing Your Workflow: Building a Personal Productivity Stack

The section covering Categories of Productivity Applications highlights what I’m getting at. There are different tools for different areas of productivity. PKM is just one of those categories (along with task management, emails, calendar, time tracking, password manager, etc.)

How will J.D. play into all of this for me? Not sure yet.

Those are my thoughts for now. I will be coming back to this forum, maybe on a different thread, to detail how I end up implementing my system.

Shortcuts at the local device file level will break. I’m not 100% sure why I even suggested that. You can create links to Obsidian notes and/or Zotero files which shouldn’t break (at least on the same system). It was most likely that.

If you have files on OneDrive you can create a share link to a file which is a URL and paste that wherever you need it. They won’t break if you rename or move the file, but of course, means f

All of this is fairly fluid. The key word is “Personal” knowledge management, not “Public” knowledge management. So do what works best for you.

I’ve found the ACE frame work is good for high level organisation with Obsidian. These are 100% my notes. Outside of that is the Zotero filing. These documents are those which suit filing eg. D&D modules, but also are the files most likely to be needed by someone else in the family. So in Zotero, they are external to my personal files. I then use JD as the common index between them.

Right now I’m using