Bit.ai

I use Joplin every day for taking my own technical notes, often with screenshots. I use it across multiple devices and operating systems that sync through Dropbox. Notes are exported to PDF when there is a need to share them, which is infrequent.

Zotero looks keenly focused on managing research information and creating bibliographies. I am not actively involved in research, but I just downloaded and installed it on my M1 MacBook Air out of curiosity.

I opened the Zotero app, tried to create a new folder, and it immediately froze. It also looked outdated. Hope you have better luck with it.

Hello,

I am also looking for something similar to this, and have to say that I have also not found it yet :/ But I will offer you my workflow, which comes as close as possible (to my knowledge)

1. Add source to Zotero with the Firefox addon
2. Organize, edit, read and annotate in Zotero (it has some great plugins and it comes with syncing, so its not only local)
3. Once read and annotated, export annotations as markdown into Obsidian vault. For this I highly recommend to use different colors for different markdown styles (I have some colors for headings, some colors for normal annotations, some for important annotations, etc. see this guide). Hit me up if you want to get my color formatting, I can send you my template.
4. Summarize the paper inside Obsidian at the top of the file
5. And then basically use the Zettelkasten method of organizing knowledge, forming it into concept notes when needed etc.

This is of course not as sweet as one single solution, but it works quite well for me. The best part is, when you export the Zotero annotations as markdown, it preserves zotero links inside the markdown file, which directly take you to the location of the quote in the PDF. This is really a game changer for me and lets me jump instantly back into a paper when I need it.

Here is an example of a markdown file after export. The headings are included and formatted automatically. The quotes are formatted as quotes and the note that I add to an annotation are also automatically added as clear text. This way I can include #tags even inside Zotero. And then you can see the links going directly into the right location of the zotero PDF.

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I hope this helps, as it is actually quite a nice setup!

I use zotero with logseq and synchronize everything between my devices using syncthing. It’s all pretty easy to set up with little research, I think.

Logseq has a good integration with zotero and lets you annotate pdfs directly in it (although the notes stay in logseq, not on the Pdf). It’s also good to link themes and topics with certain papers (e.g., papers on accessibility). I find it pretty easy to find papers like that.

Some plugins help “make it yours”. But I can’t link to them now.

Zotero, as you’ve found, comes pretty close except it doesn’t do markdown. You can host your own WebDAV server to host the PDF files for sharing. Just change the file path in the preferences.

I, Librarian is another that comes close. Works pretty much like Zotero except it has no dedicated desktop client. Everything is stored on the server. And still no markdown.

Is paperless-ngx useful for this too?

I’ve been a happy Zotero user for 6+ years, I strongly recommend it.

Hi,

I am actually currently in the process of starting a startup/product that develops something like this. Totally haven’t thought about making a self-hosted version, but that could definitely be an option!

If anyone would like to help us out and fill in our survey where we identify the key frustrations that people have, here is the link: https://tally.so/r/wMN2Wl

It would help us a lot, and hopefully, we’ll be able to offer a useful product based on this soon!

Anytype (ex Logseq and Obsidian user here)