excalibrain VS logseq

Refer: Obsidian Search, How I Use Embedded Queries, Dataview, Excalibrain

It does not represent links in graph view, but excalibrain is a plugin that will visually show relations between files depending on your own ontology. You could define „treatment“, „disease“, and „side effect“ as your own ontological categories, and define how the links between those categories will be displayed (colors, labels, line types, etc). It takes a bit to understand, but it‘s extremly powerful and customizable.

It doesn't kill the graph, especially in its current state. Currently the canvas does not automatically show relationships between your notes. And even when/if the canvas gains the ability to do that, it probably won't kill off this graph.

Dataview + Datadraw = ExcaliBrain. It's a powerful plugin for aggregating and contextualizing notes by pre-defining relationships and keywords. This ExcaliBrain demo/explainer provides a concise overview of what it is and what it can do. I skipped the setup and config so go back if you need that. Side note, Nicole van der Hoeven's overview of obsidian is a fantastic primer and her youtube tutorials are very accessible.

However there is the Excalibrain community plugin that offers a different way of visualizing links between notes (like a fancier version of the native local graph), and you can customise how certain types of links would appear in the visualization

Happy to share some of what's been working for me. Some of this is stuff I'm actively using, some of it hasn't quite made it into the "day to day use" yet, but I've been experimenting with. (Random personal advice: Never let your note taking tools feel like using them is work, that's the first step towards not keeping notes!)

- For fans of "outline workflows" Outliner is excellent. A whole bunch of outline/indented text movement and manipulation commands: https://github.com/vslinko/obsidian-outliner

- For easily refactoring notes that are getting too large you want to have Note Refactor. It gives you tools to easily take blocks of text and quickly cut them out into new notes. Its not magic out of the box, but its a powerful tool you can use when building workflows with other plugins. https://github.com/lynchjames/note-refactor-obsidian

- Local images is another good one, working with online content can get messy when you copy notes and then want to be able to work any where you have Obsidian synched. I've got it on my Laptop, two desktops, phone and tablet... I want to carry as much of my related content with me so having an easy way to convert remote images to local copies is a big productivity boost when making notes about content from the internet. https://github.com/aleksey-rezvov/obsidian-local-images

- For analysing the content for some useful stats there's: https://github.com/SkepticMystic/graph-analysis but this is for a relatively specific sort of analysis.

- More general and flexible analysis and graph visualisations are available from the combination of https://github.com/zsviczian/excalibrain , https://github.com/blacksmithgu/obsidian-dataview and https://github.com/zsviczian/obsidian-excalidraw-plugin ... in short query your notes and note metadata like its a database, build reports and data visualisations, and then excalibrain is a whole thing built on top of that power.

- Dynamic embeds of outside content are available from https://github.com/dhamaniasad/obsidian-rich-links and https://github.com/Seraphli/obsidian-link-embed depending on the style and use you like. While there is a built in functionality to preview the links to other notes when you hover over them https://help.obsidian.md/Plugins/Page+preview which has a demo here https://youtu.be/dmnVml_jbsQ?t=222

- And a real force multiplier is adding https://github.com/Taitava/obsidian-shellcommands to your setup. It lets you run scripts and prompt for information and really invest time in procedural automation without having to build your own javascript plugins. So you can setup your system so that when you use the refactor to cut out a new note, the automations will trigger, ask you to give the note a new heading, tags, and you have a little script that checks last modified time of the folder tree of text files, and looks at the folder of the last modified time and asks you in that popup if you want to move the new note to the folder the note you cut it from is located in. Or anything else you can imagine using outside automation and scripting tools on your plain text markdown files.

These are just a start and if you haven't already browsed the plugins at https://obsidian.md/plugins I wholeheartedly recommend it, people are adding new cool things pretty often and other plugins add new functionality that makes them worth checking out if they were previously not something that you found interesting. I do a read through of the plugin list probably at least once every month or two just to see what's new, and more often if I'm experimenting with changes to my workflow.

The screenshot mid-page on this web page shows what it's like to show a portion of a graph using the Excalibrain plugin which also shows content in graph form

For visualizing connections, and making graphical notes, you might consider the Excalidraw and Excalibrain extensions.

Excalibrain: A graph view to navigate your Obsidian vault

Check out the ExcaliBrain plugin: https://github.com/zsviczian/excalibrain

Logseq support via our Logseq Plugin

Sorry, but _what exactly_ «it seems to do» from your point of view?

My «second brain» now is almost 300Mb of text, pictures, sound files, PDF and other stuff. As I already mentioned, it contains tables, mathematical formulae, sheet music, cross-references, code samples, UML diagrams and graphs in Graphviz format. It is versioned, indexed by local search engine, analyzed by AI assistant and shared between many computers and mobile devices. And (last but not least) it works: it allows me to solve my tasks way more faster than with the assistant of external, non-personalized tools (like ChatGPT, StackExchange or Google).

I know no tools for all this tasks except org-mode. Well, maybe Evernote in the 2010-s was something similar — but with less features, with more bugs and with worse interface.

Personal note-taking _is_ a complex task per se (well, at least for someone like typical HN visitor). I've seen many note-taking tools, that were ridiculously featureless, stupid and inconvenient because they were _not_ complex enough.

> Sure if one wants to do emacs-gardening it is fine.

1)You can use org-mode outside Emacs. See for example Logseq (https://logseq.com/), organice (https://organice.200ok.ch/) or EasyOrg.

2)Org-mode works in Emacs out of the box, you don't need any «emacs-gardening» to use org-mode.

3)The term «Emacs-gardening» itself sound a bit like hate-speech for me. The complexity of Emacs customization is overrated, mostly due to opinions of people who never used Emacs or used it in the previous millennium.

Obsidian is great.

For those looking for an open source alternative (or don't want to pay the Obsidian fees for professional usage) check out Logseq: https://logseq.com/

For an opensource alternative to Obsidian checkout Logseq (1). I spent a while thinking obsidian was opensource out of my own ignorance and was disappointed when I learned it was not.

1: https://logseq.com/

I use logseq to keep journal of my daily work.

While Emacs and Org mode can certainly be used for this (and, when they can't, you can always inject little python/js scripts in your emacs config to take care of specific things), I'd also recommend you take a look at Logseq.