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https://github.com/wikibonsai/wikibonsai

A jungle gym for thought with an API for the mind.
https://github.com/wikibonsai/wikibonsai

bidirectional-link digital-garden exocortex graph hierarchy knowledge-base knowledge-bonsai markdown note-taking ontology personal-knowledge-management personal-wiki pkm second-brain semantic-tree taxonomy wikibonsai wikilink wikiref zettelkasten

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A jungle gym for thought with an API for the mind.

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README 

        
# WikiBonsai



[![A WikiBonsai Project](https://img.shields.io/badge/%F0%9F%8E%8B-A%20WikiBonsai%20Project-brightgreen)](https://github.com/wikibonsai/wikibonsai)



> A knowledge bonsai wends through concepts in semantic space, like a melody winds through harmonies in music.



###### [cite me!][wibomd-doc-cite-this]





  




> ⚠️ Please remember to backup all data and use version control.



The WikiBonsai project[^ai] transforms a collection of markdown files into a text-based, easy-to-navigate [jungle gym for thought][wibomd-doc-philosophy--a-jungle-gym-for-thought][^mind] with an [API for the mind][wibomd-doc-design--an-api-for-the-mind][^mixed-metaphors]. This is accomplished by enabling personal knowledge management (PKM) workflows that rely on `[[wiki]]` syntaxes, "semantic trees" or "knowledge bonsais", and data visualizations that are viewable on screens or in augmented/virtual reality.



This project is about strategically implementing and open-sourcing functionality that will benefit the most users and developers across the digital ecosystem. Thus, it abides by the [Unix Philosophy][art-unix-phil]: Everything is modularized and implemented in such a way as to maximize re-use whether it be for the browser, desktop, mobile, or headset. It's about furthering the state of PKM as a whole by building atop "[standardization bedrock][wibomd-doc-design--drilling-down-to-standardization-bedrock]" instead of just creating a single application.



Further, these workflows may also facilitate the mapping of [semantic space][wibomd-doc-design--semantic-space] which could prove an invaluable resource in building a better understanding of how neural nets work and furthering the development of interpretable, explainable AI.



Only time will tell how far this path may [go][wibomd-doc-philosophy--finding-free-will].



## Notable Workflows



These are the workflows the WikiBonsai project enables for markdown-based collections of notes:



1. Expanded [`[[wikirefs]]`][wibomd-repo-wikirefs] syntax for quick associative linking (a.k.a. "wikilink", "bidirectional link", "[internal link][mediawiki-internal-link]", etc.).

2. [Mechanics][wibomd-repo-semtree] to cultivate and train a unified "[semantic tree][reddit-musk]" or "knowledge bonsai" across a collection of markdown files.

3. A clean, lean, [yaml][yaml]-like [markup language for structured attributes][wibomd-repo-caml-mkdn] (with built-in `[[wikiref]]` support).

4. [Graph][wibomd-repo-treehouze] utilities to experience and interact with a unified visual-spatial "[memory palace][memory-palace]" that emerges from the relationships formed across markdown notes (syntaxes 1 + 2).



These workflows are what distinguish "WikiBonsai" from other styles of digital garden -- particularly the [semantic tree][reddit-musk].



## Project Info



### Docs



The documentation in this repository describe the philosophies, mechanics, and terminologies that are adopted throughout all of the WikiBonsai projects:



- For Use:

  - [Getting Started][wibomd-doc-use]

  - [Privacy and Security][wibomd-doc-secure]

- For Dev:

  - [Design Principles][wibomd-doc-design]

  - [Terminology][wibomd-doc-terms]

  - [Code of Conduct][wibomd-doc-code-of-conduct]

  - [Contributing][wibomd-doc-contributing]

- For Lore:

  - [Guiding Philosophy][wibomd-doc-philosophy]

  - [Origin Story][wibomd-doc-story]

  - [Citations and Sources][wibomd-doc-cite]

- For Input:

  - [Questions][wibomd-doc-questions]



### Repos



The following links point to repositories of the WikiBonsai project and are organized by stack depth. Projects toward the top are ready-to-use and meant for the end user, while projects toward the bottom are meant for developers to build with and integrate into other solutions:



- For Use:

  - AI:

    - [germinator][wibomd-repo-germinator]: An AI-powered semantic seedling [germinator][demo-germinator] that generates starter semantic mappings of concepts which are easily transplantable into one's own digital garden.

      - [semtree-germ][wibomd-repo-semtree-germ]: An earlier version of the germinator that focused on [semantic trees][demo-semtree-germ].

    - [tree-trainer][wibomd-repo-tree-trainer]: An AI-powered [tree trainer][demo-tree-trainer] that generates syntax trees for sentence(s).

    - [prompt][wibomd-repo-promp]: Prompts for AI-powered digital gardening.

  - Notes:

    - [vscode-tendr][wibomd-repo-vscode-tendr]: A [VSCode][git-vscode] extension for tending a WikiBonsai digital garden.

    - [tendr-cli][wibomd-repo-tendr-cli]: A CLI tool for tending a markdown-based WikiBonsai digital garden.

  - SSG:

    - [jekyll-garden][wibomd-repo-jekyll-garden]: A [jekyll][ssg-jekyll] template that can be imported as a gem or cloned as a template project.

    - [jekyll-bloomz][wibomd-repo-jekyll-bloomz]: An example setup to enable WikiBonsai workflows fro a [jekyll][ssg-jekyll]-bsaed statically generated site (SSG).

    - [astro-bloomz][wibomd-repo-astro-bloomz]: An example setup to enable WikiBonsai workflows for an [astro][ssg-astro]-based statically generated site (SSG).

    - [eleventy-bloomz][wibomd-repo-eleventy-bloomz]: An example setup to enable WikiBonsai workflows for [eleventy][ssg-eleventy]-based static site generation (SSG).

  - Starters:

    - [garden-beds][wibomd-repo-garden-beds]: A collection of starter WikiBonsai digital gardens -- includes starter markdown files and config files.

- For Dev

  - Markdown Parsers:

    - [markdown-it-caml][wibomd-repo-markdown-it-caml]: A [markdown-it][git-markdown-it] plugin to enable  `:colon::attributes`.

    - [markdown-it-wikirefs][wibomd-repo-markdown-it-wikirefs]: A [markdown-it][git-markdown-it] plugin to enable `[[wikirefs]]`.

    - [remark-caml][wibomd-repo-remark-caml]: A [remark][git-remark] plugin to enable `:colon::attributes`.

    - [remark-wikirefs][wibomd-repo-remark-wikirefs]: A [remark][git-remark] plugin to enable `[[wikirefs]]`.

  - Jekyll:

    - [jekyll-graph][wibomd-repo-jekyll-graph]: A jekyll plugin to generate graphs of blog content.

    - [jekyll-semtree][wibomd-repo-jekyll-semtree]: A jekyll plugin to generate a semantic tree from index collections.

    - [jekyl-wikirefs][wibomd-repo-jekyll-wikirefs]: A jekyll plugin to enable `[[wikirefs]]`.

  - Base:

    - [caml][wibomd-repo-caml-mkdn]: Base utilities for Colon Attribute Markup Language (`:colon::attributes`).

    - [caudex][wibomd-repo-caudex]: An index to cache and store WikiBonsai relationships.

    - [semtree][wibomd-repo-semtree]: Base utilities for "semantic tree" or "knowledge bonsai" building in markdown.

    - [treehouze][wibomd-repo-treehouze]: Generalized graph utilities with minor specialized features for visualizing WikiBonsai-enabled markdown-based PKMs.

    - [wikirefs][wibomd-repo-wikirefs]: Base utilities for internal links (`[[wikirefs]]`).

  - Spec:

    - [caml-spec][wibomd-repo-caml-spec]: Test suite for Colon Attribute Markup Language, CAML, (`:colon::attributes`) specification.

    - [wikirefs-spec][wibomd-repo-wikirefs-spec]: Test suite for wikirefs (`[[wikirefs]]`) specification.



## ⚠️ Usage Note



The systems you interact with have an effect on the way you think. This system is meant to provide a ["jungle gym for the thought,"][wibomd-doc-philosophy--a-jungle-gym-for-thought] but it can't do everything and might even have negative consequences if used improperly. Here are some supplemental suggestions for adopting a PKM-framework such as this, especially for educational purposes:



### Write Full Essays



The workflows this project enables are meant to help develop an explicit relationship with the words you use. It's possible over-reliance on a tool like this (like many other digital productivity tools) can allow, or even facilitate, overly modular and fractured trains of thought. Writing [full essays][utb-essay] can combat fractured thinking and exercise those parts of the mind.



### Refer to Common Cultural Reference Points

###### (such as [britannica][britannica] or [wikipedia][wikipedia])



By adopting a tool specifically meant for mapping vocabulary, it can be tempting to use niche words or make up one's own to demarcate an idea. But too much of this risks building a Tower of Babel and losing the ability to communicate effectively with others. Use shared vocabulary where you can and if you've found a word of better fit, use it with others. That is the purpose of language after all.



### There is Never a "Final Word"



Like this project it is best to view a set of notes and explicit knowledge as a current state of affairs -- it's the state of the trail; of how much clutter has been cleared away. The goal is to build a navigable path for yourself, but to remain aware of what other things lie beyond the already-explored path. Always be open to what hard reality is telling you, especially while getting your hands dirty.



### Get Your Hands Dirty



The digital world cannot replace practical, hands-in-the-mud experience. No matter what you learn or study be sure to learn something, _anything_, that requires your hands in the real world.



## Forward



Here's to making the road ahead a touch less bumpy and a bit more wonder-full for those that follow.



[**just keep tending...🪴**][wibomd-doc-use]



[^ai]: 🤖 AI Collaboration: To date, code and prose of the WikiBonsai project was not written by AI, but was _occasionally_ consulted to improve overall quality. This may or may not change going forward.

[^mind]: Not too dissimilar from a ["bicycle for the mind"][utb-mind-bike].

[^mixed-metaphors]: Please excuse the mixed metaphor soup.



[art-unix-phil]: 

[britannica]: 

[demo-germinator]: 

[demo-semtree-germ]: 

[demo-tree-trainer]: 

[reddit-musk]: 

[git-markdown-it]: 

[git-remark]: 

[git-vscode]: 

[mediawiki-internal-link]: 

[memory-palace]: 

[ssg-astro]: 

[ssg-jekyll]: 

[ssg-eleventy]: 

[utb-essay]: 

[utb-mind-bike]: 

[wikipedia]: 

[yaml]: 



[wibomd-doc-cite]: 

[wibomd-doc-cite-this]: 

[wibomd-doc-code-of-conduct]: 

[wibomd-doc-contributing]: 

[wibomd-doc-design]: 

[wibomd-doc-design--an-api-for-the-mind]: 

[wibomd-doc-design--drilling-down-to-standardization-bedrock]: 

[wibomd-doc-design--semantic-space]: 

[wibomd-doc-philosophy]: 

[wibomd-doc-philosophy--a-jungle-gym-for-thought]: 

[wibomd-doc-philosophy--finding-free-will]: 

[wibomd-doc-questions]: 

[wibomd-doc-secure]: 

[wibomd-doc-story]: 

[wibomd-doc-terms]: 

[wibomd-doc-use]: 



[wibomd-repo-astro-bloomz]: 

[wibomd-repo-caml-mkdn]: 

[wibomd-repo-caml-spec]: 

[wibomd-repo-caudex]: 

[wibomd-repo-eleventy-bloomz]: 

[wibomd-repo-garden-beds]: 

[wibomd-repo-germinator]: 

[wibomd-repo-jekyll-bloomz]: 

[wibomd-repo-jekyll-graph]: 

[wibomd-repo-jekyll-semtree]: 

[wibomd-repo-jekyll-garden]: 

[wibomd-repo-jekyll-wikirefs]: 

[wibomd-repo-markdown-it-caml]: 

[wibomd-repo-markdown-it-wikirefs]: 

[wibomd-repo-promp]: 

[wibomd-repo-remark-caml]: 

[wibomd-repo-remark-wikirefs]: 

[wibomd-repo-semtree]: 

[wibomd-repo-semtree-germ]: 

[wibomd-repo-tree-trainer]: 

[wibomd-repo-tendr-cli]: 

[wibomd-repo-treehouze]: 

[wibomd-repo-vscode-tendr]: 

[wibomd-repo-wikirefs]: 

[wibomd-repo-wikirefs-spec]: 





  🇺🇸 Made in the USA 🦅 🐊