In fact my data is already split between Semantic Synchrony[1] and org-roam[2], and it's a bummer.
May I recommend an organized note taking system copying the literal text and link for reference. I like org-roam with a hotkey to capture title and if existent any highlighted text.
https://github.com/org-roam/org-roam
There are of course about a million ways to skin this particular cat and plenty of them are good.
The benefit of using your own system is that you can trivially reference information from many websites via one method instead of relying on the many and varied features of many sites. The benefit of copying the full relevant text is both that you can search that text and if a site or a comment goes missing tomorrow or 5 years from now you aren't out the information.
I'm a freedom-respecting software (the F in FOSS) philosophy activist. I agree that developers need to make money and capture value for software development to be sustainable.
I believe Roam is unethical because the incentives between the user and the proprietor are misaligned in Roam's business model, where a monthly fee is required to continue using the software.
Feel free to ask me any questions on why I consider Roam unethical, digital ethics, or the free software philosophy.
For those looking for other knowledgebase management software, look at freedom-respecting (and open-source too) software: Athens Research[0] (YC20), org-roam, and logseq. If you'd like extensibility, try org-roam.
[0]: https://athensresearch.github.io/athens/
[1]: https://github.com/org-roam/org-roam
[2]: https://logseq.com
I started a draft describing my 'process' [2], but it's pretty incomplete.. there are some bits scattered across exobrain too.
Also lately I started playing with Logseq [3] to get a more interactive representation of exobrain [4] (warning, it's pretty heavy, needs some optimization and I might have messed up the physics). Logseq could be a great gateway for people who want to get into org-mode but not ready to go 100% Emacs, highly recommend to try it it!
[0] https://github.com/org-roam/org-roam
[1] https://beepb00p.xyz/pkm_processing.html
[2] https://beepb00p.xyz/pkm-search.html
After lots of trial/error and at the end of the rabbit hole I found Emacs with org-roam [2].
It has a steep learning-curve and often seems outdated, but it is also very powerful, has VIM hotkeys, and allows me to create the academic workflow I want - so far I can automatically create a note from my Zotero .bib library, fill it based on a template and the insert all my annotations from the associated PDF. Afterwards I also semi-automatically extract the references from that PDF, insert them into the annotations and then start to link everything into my Zettelkasten system.
Sometimes I wish I just stayed with VSCode/Markdown, but then I remember that I can now put "elisp" on my resumee :)
Overall I think that the "new" note-taking/Zettelkasten-systems is very cool and useful, but I wish someone would come along and create "the next big thing" which in my opinion is multi-dimensional notes.
Tiddlywiki/Tiddlyroam [4,5], TheBrain[6] and even Scrivener [7] seem like a step in the right direction, but they also make some other things overly complicated (convoluted UI, no plug/play export, bad editors, ...).
I want to be able to freely take notes on my computer the same way I can do on paper, and then be able to "super-charge" them by linking, aggregating, searching them. At the moment notes are "one-dimensional", i.e. I can only write from top to bottom. Compare it to paper where I can freely change my style of writing, add drawing, annotations, change directions, ... Writing on the computer just feels very restricting.
1: https://dendron.so/ 2: https://github.com/org-roam/org-roam 3: https://github.com/inukshuk/anystyle 4: https://tiddlywiki.com/ 5: https://tiddlyroam.org/ 6: https://www.thebrain.com/ 7: https://www.literatureandlatte.com/scrivener/overview
If anyone is interested in open source options, I'd recommend:
Foam - A Roam-inspired tool for markdown note taking--ahem, personal knowledge management (same features as Organizedly)--that runs on VSCode/Codium. I personally use and love it. Syncs across all my devices with Git, and deploys easily on free-tier Vercel, which is a nice way to check my agenda or read a note on my phone. https://foambubble.github.io/foam/
org-roam, for those emacs/org-mode people. I always wish I had the fortitude to become productive in emacs, but it seems it never will happen. https://github.com/org-roam/org-roam
Because of it's popularity someone created an org-mode package called org-roam [1] that does some of the things that roam does, but in emacs. These are not officially related though.
* org-roam: https://github.com/org-roam/org-roam
* Obsidian: https://obsidian.md/
* Athens: https://github.com/athensresearch/athensOrg gained new features too in the last ten years. E.g. for crosslinking there is org roam: https://github.com/org-roam/org-roam
I was also in a similar position trying to decide between TiddlyWiki, Notion, Evernote, OneNote, Confluence, etc, for a personal knowledge base, but eventually settled on org-mode. Lots of people use it for managing TODOs, planning, and organising things, but I use it as a personal knowledge base.
org-mode out of the box supports hierarchical note taking with headings and links to other files or headings. You can also use org-roam (https://github.com/org-roam/org-roam) to get something like a Roam or Zettelkasten workflow (with backlinks etc) without having to use separate software (since you said "I plan on keeping a personal wiki and then taking out core ideas from them into my zattlekasten" maybe you will find this useful). If your notes include references/links to academic papers, then you'll love org-ref (bibtex integration).
If you're interested, I'd recommend having a play about with vanilla emacs and the Doom Emacs configuration (https://github.com/hlissner/doom-emacs).
It's definitely more work to set up than Notion, but much more customisable and you're in full control of your data (and can store everything under version control!). I've not used TiddlyWiki enough to form a useful opinion though.
On the contrary, if you are reading papers and doing research, taking notes in a meaningful way is more helpful than you would realize. The human brain tends to skip information while reading and you only realize you didn't actually understand that part when you try to write it yourself. The note-taking part doesn't actually take that much brain resources. I am not a native English speaker but I am taking my notes in English. While taking my notes I don't care about grammar or anything, I just read and write what I understood. When I finish the paper and I am comfortable with the topic, I return to my notes, fix grammars and, link them with my other notes. For example, sometimes I come up with a research idea, I make a note about it. In the future, while reading a paper, I realize some of the techniques that are described in the paper might be beneficial to that idea so I link them together.
In conclusion, it really depends on your area of work whether to take regular notes or Zettelkasten notes. Forcing your workflow to these methods might hurt your productivity but if you are a researcher I can say, it will be beneficial.
I recommend reading "How to take smart notes" book if you are interested in the topic.
I am using https://github.com/org-roam/org-roam to take my notes, https://github.com/org-roam/org-roam-server to visualize it.
See "org-roam" [1,2] (and several blog posts and youtube videos by now)
[1]: https://github.com/org-roam/org-roam [2]: https://blog.jethro.dev/posts/introducing_org_roam/
When I found Roam Research I had two thoughts: 1) wow, this UI is rather polished and the UX is very good too and 2) it would be quite annoying if Roam Research disappeared after I had put in a lot of effort in my database and became familiar with the editor and UI/UX affordances. I know you can export the Roam database to a quite sensible JSON/Markdown format, but if I can't self host the editor I will always be worried about this.
Basically this was a a deal breaker for me so I looked around for alternatives and found org-roam[1]. It's an Emacs package that gives you a similar workflow for creating notes, inserting links to notes, viewing note backlinks and a few other things. It's easier to get into the org-roam ecosystem if you already either use Emacs or vim, but I know a lot of people that have started using Emacs just to use org-roam.
There's a quite high learning curve compared to Roam Research but you have the certainty that it won't disappear from one day to the next :)
I don't want to be too much of an Emacs/org-roam evangelist because it's definitely not for everyone, but here are some of the workflows I do regularly:
1. Have a 'daily notes' file where I initially write most kinds of notes; for example when I change the configuration of a system I'm working on, lecture notes, or pretty much anything else. I can insert inline images and attach any kind of file to each of these headings.
2. Refile those daily notes into dedicated notes and link them to other relevant notes. For example, I would link the file containing my notes for a given lecture to the top-level note for that class, etc.
3. Manage the research notes for my master's thesis. I actually have a pretty cool workflow here:
- I find interesting papers or websites online and capture them into Zotero[2] using the browser extension. This automatically creates a fully populated entry in my .bib file and downloads the relevant PDF or snapshot of the website into my local storage.
- I then use helm-bibtex[3] in combination with org-roam-bibtex[4] to create and easily access my notes on this particular bibliographical source. This note is just like any other org-roam note, so it can contain forward and backward links, etc.
- And finally, I use org-noter[5] to read the PDF and make notes on each page or paragraph. These notes are simply plain text entries on the bibnote. This is pretty huge for me, because it gives me a very focused interface for reading and processing what is being said in the article while I make detailed notes about it (which helps recall and understanding). And also, finding exactly where in the source a given note came from is literally one keyboard shortcut away.
In conclusion, it's a lot of up-front learning and tweaking to get your knowledge management system just right for you, but it may be worth it for some people. BTW, feel free to join the org-roam Slack - there are a lot of people there who are very willing to help.
[1] https://github.com/org-roam/org-roam
[3] https://github.com/tmalsburg/helm-bibtex