Using JD in a Digital Garden

My foray into the JD system is going well. It’s been quite easy to reorganise information that was already pretty organised in the first place. Good news is there is more “rightness” about it now.

(5 minutes of thinking and I’m still not sure what question I’m asking for help with!)

I have a well established digital garden in Obsidian, which bleeds into my website. There is a mix of source material (articles, books etc), plus my written comments on those. I’ve organised the website around 4-5 major landscape areas (fits the digital garden theme).

They are:

  • Expand My Way of Being — My Way of Being is more than the behaviour I show. It’s the total sum of how I engage with the world, make meaning from my environment and take action. Expanding my Way of Being by being a learner in the world creates new possibilities for me to move forward in life.
  • Hobby Together — Here’s where I share my progress on whatever project currently takes my fancy, plus any relevant discussion on supporting technologies.
  • Productive Laziness — There is art in doing as much as possible, as easily as possible and that’s what I call being productive lazy. It’s the term I use to describe my approach of doing as much as possible with as little effort as possible and applies particularly to repetitive tasks where I want them done quickly and without having to think too much. There is too much going on in my world to allow thinking where I don’t need to.
  • The Garden Shed — Every garden needs a good shed, full of the right tools to make it flourish.
  • Quantum OS — my operating system which in no way suggests I am a computer. Rather, it is a set of notes that describe the rules and standards I have determined are best to manage my digital information as I see fit.

While they are suitable for organising a website, they don’t fit as well into a JD system because this is only what I’m chosing to publish. The background articles, literature notes etc aren’t covered.

Somewhere in my garden I have this library structure:

Section Description
000 Knowledge Management
100 Personal Management
150 Hobbies and Pastimes
200 Philosophy & Psychology; Spirituality & Religion
300 Social Sciences
400 Communications & Rhetoric; Language & Linguistics
500 Natural Sciences
600 Applied Sciences
700 Art & Recreation
800 Literature
900 History & Biography & Geography

Too many Areas there as I will chew a couple up for personal use and I don’t want to have multiple project-equivalent systems.

(yes, still not sure of the question - thinking out loud)

Obsidian, my website and Zotero all let me tag and item multiple ways so I do have some flexibility. Tagging is metadata, not what something is about.

I have to get this organisation right before I start. I know from experience it’s too costly to change.

The level 3/4 items are what I’m concerned about. Does going broad at the top level constrain me later on. Does going specific at the top level mean I exceed the (nominal) bounds of the system?

In the end, it may be a question of finding the right taxonomy. What do you think?

Thanks, David

Hi QuantumGardener, I took a look at your site. I love the idea of a digital garden.

Too many Areas there as I will chew a couple up for personal use and I don’t want to have multiple project-equivalent systems.

So if I understand correctly, you are having trouble deciding what the proper scope of your project will be. That is, what should belong in your JD system and what shouldn’t? And you are also saying that you don’t want to duplicate information in multiple places?

The level 3/4 items are what I’m concerned about. Does going broad at the top level constrain me later on. Does going specific at the top level mean I exceed the (nominal) bounds of the system?

Well, in a project, you have ten areas at the top level and ten categories in each area, for a hundred categories in total, along with up to a hundred IDs in each category. Two points come to mind:

  1. Take your time thinking about the scope of your project. Is it your life? Is it just for your learning and your website? Try to have a clear idea of what problem you’re trying to solve by implementing this or any particular organization system.
  2. When choosing your categories, imagine a folder in a filing cabinet. How much would that folder hold? Would it be too large (i.e. too general) or mostly empty (too specific)?

For the first point, I wanted to organize my files because I kept losing things like scans of passports and IDs which I need because of my international marriage. I knew those documents could be in multiple places, so I also needed to address this. I started thinking about what my JD system would look like based on these ideas. I thought about it for about a week and a half before I started making my areas and categories.

For the second point, I needed a place to keep physical copies of documents, and I opted for a filing cabinet (actually a filing box, if you will). The limitation of an actual file folder helps narrow down what belongs in its own category.

I’m also a student and a lifelong learner, so I’m still considering how these things will fit into my system and whether they deserve their own project. For some things, the answer is clear because the knowledge is practical, clearly relating to some personal goal I have. For example, notes about nutrition and fitness should go in a category in my Health area. I’m less clear about how my MBA course notes fit in, though. Maybe they are out of scope. I mean to say that the two points above have helped me achieve my stated goals, but the resulting system hasn’t been a panacea for all my organizational needs. Nonetheless, I hope I’ve been of some help.

A knowledge project

Something that occurred to me is that the indexing system used by the bullet journal has worked quite well for my notes in the past, so I may stick to that for my MBA notes. I may take up the idea of numbering the index entries to make cross-referencing within and between physical notebooks easier.

I envision the following as one way you could develop this as a JD project called “K01 Knowledge and learning.” Below is my train of thought on how I’d develop such a project in my own context.

Each notebook (one per class) could count as a category, and each index entry in the notebook could be an ID. Then, the area would be “MBA.” That’s one of ten areas. Then I could have another area for each of the subjects I’m interested in, for example “philosophy,” which would have a series of different notebooks, perhaps for different areas of philosophy such as ethics or ontology, or perhaps even just for different works such as Aristotle’s Nicomachean Ethics. In these notebooks, I could write notes, reflections on the content, lists of questions I have, soliloquies, dialogues, and so on.

Each of my notebooks is A5 sized with about 60 pages, and in my experience, much fewer than a hundred IDs fit in one notebook with my past usage. Going digital, I would probably emulate this usage.

If I wanted to publish these ideas on my website, I think it would be easier to go digital with the notebooks. I don’t understand your publishing process, but you mentioned write once, publish everywhere on your website, is that right? Perhaps tags could distinguish public and private IDs in this knowledge project. Just like with my filing cabinet analogy, the physical notebook analogy may be helpful to organize your knowledge.

A website project

The setup I’ve described above would imply a different project for each of the landscapes you describe on your website, but that may be too cumbersome. It comes back to point 1 above, where the scope of your project is important. If the scope of your project is “the website,” and the mission of your website is document your digital garden of knowledge, then the following may work.

Sections 000-100 could be under the area of “The Garden Shed.” Sections 150 and 700 would fall under another area, perhaps appropriate for your “Hobby Together” landscape. The rest could fall under an area called “Expand My Way of Being.”


I hope these ideas help!

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Hi LasTr,

Thank you for you considered response. This is exactly why I prefer forums over Discord :grinning:

We seem to both be dealing with the same problem, except that you’ve solved the first part. Maybe we can get a solution to the knowledge problem together.

Scoping
Ok, you got me. I didn’t follow the advice to scope first but in my defense I didn’t fully understand what that implied until I read your post and spent some time thinking about it. One of my learning strategies with any new software tool is to test the fences and see where the weak spots are in the software and my approach. That’s what I have done in setting up some obvious areas and categories yesterday, and the weak points have been found!

Over time I’ve migrated more towards centralised systems. My main systems for managing data and information are:

  • Obsidian - text-based note taking with backlinks, tags etc. I have both personal and work vaults which are very different.
  • Zotero - document management systems for PDF files of manuals, receipts, blood test results etc.
  • Calibre - ebook management
  • Plex - tv/movie media
  • iMatch - photos and home videos

Each is very much optimised to my needs and works well. The JD promise of a centralised index enabling common reference works well for the first two, could and could serve as tags for eBooks in Calibre (ie. writing about topic X, where are the books on that?). It’s not applicable for Plex and iMatch. They are different things and easily managed by their own metadata systems.

:bulb: Since I’ve had the focus on being productively lazy and centralising systems I missed that I have multiple purposes. Intuitively I knew it (hence my discomfort and earlier post) but was unable to articulate that’s exactly what it was. When pointed to scope it out, I was presumptive in having just the one scope I was working to. Personal - not work.

Goal: Don’t split information
I don’t want to split information any more than I need to. The tools I have benefit from information collation and the ability to search or link content. I don’t know if you are familiar with Obsidian at all. It is one of many tools that provide easy connection of information. This can be through a WikiLink or tags. Obsidian has a powerful backlink function. This means that if I want to know all pages that link to Ethics, I can find them at a click. It also means that if I rename a page on Ethics to Ethical all links will update. This is very powerful and I make use of it across my personal notes and the website. It breaks immediately if I have different vaults for different JD projects.

For my website publishing I need only move a file from its original location in Obsidian into the Quartz\notes folder, run my magic scripts and it publishes. All links to and from that original article remain.

:coffee: (short break while I consider my next thoughts)

Any reader who is good at crime puzzles will have noticed the smoking gun. I have already split my main Obisidan vault into two. My knowledge/working stuff, and the Quartz publishing. All I need do is rejig some folder names with a PRJ at the front and I’m good to go. Once I’ve finished scoping that is.

I need to define the following scopes:

  • Family document management - mostly all that I have in Zotero at the moment but that will expand. Information I know where it is, need to put my hands on quickly, and if I was not around my family needs to find.
  • The website files - what’s being shared online, represents “final” writing though here I am split between more static information and blog posts
  • The Knowledge Project - whatever that is. Most of what’s in my Obsidian vault now, excluding my journal and personal history information.

I have some ideas about the boundaries and will start working them today. Nothing much else is going to happen with 39C forecast.

The Knowledge Project
I’m not sure anyone has solved this. Start working your way through category type links on Wikipedia and nothing is consistent. Taxonomy is hard and that’s what we’re dealing with. The problem compounds because each of us sees our knowledge in a different way and so we want to organise around that.

My initial thoughts are that we have 4 components to deal with.

  1. Source/reference materials - your MBA course materials, my ontological coaching notes, Plato’s writings, articles, books, quotes
  2. Our personal notes on those materials - I see these commonly referred to as literature notes. What knowledge did we gleam from the material in 1.
  3. Our outputs - the written synthesis of knowledge and wisdom from the combination of 1 and 2 (note to self: 100% of this ends up on the website)
  4. Taxonomy/classification/maps of content/tags - call it what you will, this is the organisation of the concepts within 1, 2, and 3.

There is also metadata associated with a lot of this such as author, date, format (article, book) etc.

My approach to what is currently 20-29 Hobbies\21 Video Games highlights the need to have a focus on content over form. Do I file “Last of Us: Part 2” as an article under “Playstation 5 Games”, “Adventure Games” or itself. It is all of these things but I contend Playstation 5 Games and Adventure Games are metadata about The Last of Us: Part 2. It is the subject so that’s what I create and I tag the metadata in Obsidian. I can then use it to create a list of all PS5 games with ease. If I’m writing, I’m writing about the game, not the game and format x.

I think I can pull my areas of study ok. They mostly match the Landscapes I already have in place with some finessing, plus other areas of interest. I’ll scope, begin mapping and share what falls out. At the moment I have too many crossovers eg. is Photography an area of study or part of a hobby. If a hobby, then why is Cross-stitch not an area of study.

Apologies if my post here rambles — I’m short on editing time, so I just put down my first ideas. I don’t necessarily have any good ideas for solutions to the problems we’re discussing, but I can comment with my own experiences. These are interesting problems!

Any reader who is good at crime puzzles will have noticed the smoking gun. I have already split my main Obisidan vault into two

Definitely a hard problem to solve. I think it’s hard not to duplicate information in some way or another if you want to publish writing on your website. But it sounds like the system you already have set up with Obsidian is pretty slick and streamlined already. Could this be a “ain’t broken, don’t fix it” area? I know for myself, I get sucked into all these big ideas about cool systems and web servers and all these shiny toys, but after I get it out of my system, I usually think I would have been better off with the status quo and would have done some more actually interesting stuff with that time. But that’s just me.

Scopes

Family document management

I’m surprised you use Zotero for that. For me, it would seem the filesystem (JD-conformant lol) would be a better choice. But if it works then that’s what’s important. I use Zotero for all my citations for my MBA and all my ebooks (and all 9.6GB of attachments).

You mention Calibre, which is a great program, but for one reason or another I don’t really like it much, so I only use it for converting ebooks and for deDRMing my Kindle books. Once they’re converted, they go into Zotero in their appropriate folder. I should note that my Zotero folders as of yet are out of scope for my JD system. Maybe they’ll go into my Knowledge one someday, but I don’t feel any strong need to go down that rabbit hole quite yet. I have a feeling that for my needs, the notes for the Knowledge system could probably fit just fine in my main JD system.

Currently, I have an area in my JD system 50-59 Personal/55 Document where my database files and Zotero etc. files go. It looks like this:

55 Document/
├── 55.01 Calibre
├── 55.02 Zotero
├── 55.03 Johnny.Decimal
├── 55.04 Google Drive download
└── 55.06 Sheet music

I took this idea from @fjgenieter’s post “My System per 2023-11-09” where he has 80-89 MediaData/81 Document. I thought about using the same area, but I was certain that other media types like music and pictures were clearly out of scope for me, so I just took that category and stuck it in my Personal area. My music is already well managed by beets, and my pictures by Darktable. (For my pictures I just wrote a script to rename files based on date, and I use Darktable to create subfolders with a descriptive name of location or purpose per shooting session in each year’s folder.)

I should mention that I don’t use Zotero’s paid storage service. Instead, I sync Zotero’s storage directory to my phone and my Raspberry Pi with Syncthing.

Sorting knowledge

Taxonomy is hard and that’s what we’re dealing with. … If I’m writing, I’m writing about the game, not the game and format x.

I agree. I think the JD system’s strength is in the limitations on depth. A shallow depth makes you make choices about what’s important and it helps in pruning the folder tree. With a shallow tree, you have a lot of leaves on each branch, but with a deep tree, your branches risk looking anemic. The information is all the same, nonetheless.

Photography an area of study or part of a hobby. If a hobby, then why is Cross-stitch not an area of study.

I’ve seen Johnny suggest on other posts in this forum that perhaps this is a sign that these areas or categories are candidates for merging. The whole point is to help find your stuff, so it’s best to eliminate as much ambiguity as possible by removing or combining similar choices.

Heyy, thanks for the ref. Glad you got something from it :slight_smile:

I’m surprised you use Zotero for that. For me, it would seem the filesystem (JD-conformant lol) would be a better choice. But if it works then that’s what’s important. I use Zotero for all my citations for my MBA and all my ebooks (and all 9.6GB of attachments).

You mention Calibre, which is a great program, but for one reason or another I don’t really like it much, so I only use it for converting ebooks and for deDRMing my Kindle books. Once they’re converted, they go into Zotero in their appropriate folder.

It’s true, I could use a folder-based hierarchical file system instead of Zotero but it gives me two advantages. Firstly, I store the files on a locally-hosted webdav server that I can securely access from outside. This solves the problem of storing more private information in a cloud. Secondly, it gives me metadata. I would think that’s the value for you and your research citations. Like you I only sync the database and not the files.

Calibre is backed by calibre-web, also locally hosted. I treat ebooks the same as you except I leave them in Calibre. The books and calibre database are locally-hosted on my NAS. This gives me access for basic lookup from anywhere in the house. I don’t need to be at the PC where I run Calibre. Again, the benefit here is metadata. Have I read this book yet? What series does it belong to? Who are the authors? A flat file system can’t manage that.

The message I see time and again with JD is, “so I know where to store/find it” and that’s valuable. The JD setup I have worked on so far has greatly clarified things. But, and this is where we’re getting tripped up with “knowledge” storage, is there is only 1 point. We have to choose and that creates a cognitive hiccup when a document can be in multiple places.

In Zotero I have bank statements that show USD conversions. I need these at tax time. The receipt gives me a price in USD, but I pay my taxes in AUD. Because Zotero isn’t a flat file system - every item has it’s own unique folder with the files within - I can have a particular bank statement appear under the bank category, and this year’s tax. JD makes it clear which Zotero collections I need to work with. It can now only be in one of two places, both of which are 100% valid.

That brings us to Obsidian. On the face of it, Obsidian is a note-taking tool. Add backlinks, folders, tags, properties and plugins like Dataview and it is clearly also a system that manages meta-data. As important as the content of a note is its relationship to other notes. The actual storage location of the file on disk means very little. Folders are a super-high categorisation for convenience.

At the weekend I tested building a matching JD structure in Obsidian. It doesn’t work that well. Better is tagging notes with the JD hierarchy (nb: decimal points in tags aren’t allowed so there is a slight conversion needed, but if my index is in Obsidian I can just link back to that).

Moving a file from one folder to another i.e from where it’s written originally, to the Quartz publication notes folder for my website breaks absolutely no semantic meaning. The only thing I may have to change is some code to filter out tags I don’t want to display on the website.

I get more advantage from having notes interconnected within Obsidian (wherever they are) than I gain from the organisation structure of JD as a hierarchy.

JD’s AC.ID flags are simply metadata on a note. They are what is important, not the underlying file structure.

Time to keep plugging away at it and time will tell. PKM is never static.

Greetings from a newbie (that is, this is my first appearance in this forum).

Have you found a solution?

I’m on the same boat.
Though I’m not a researcher, my content production relies heavily on academic papers and similar.

I still have to implement the JD to my System, but I had the same concern: how do I manage content that may go into several categories?

So I had an idea (still to be implemented): adding the codes of the several categories inside the filename, so that I can find the documents by searching for the specific code (I’m on Mac, so I may use Spotlight as well as Alfred).

So I have the usual Index for reference, I also may put the papers in their “main category”, but I still keep the flexibility by using the filenames accordingly.
Something like tags or hashtags.

I repeat: I haven’t started with the JD System yet: I’ve only read the website and the workbook right now.

I’m open to discussion and further suggestions.