Hi, im looking for a tool that helps me organize my research papers and PDF-library, embed their PDFs, let me comment/highlight inside of them, and also add more text around them. Preferably have it running as a selfhosted server, or accessing shared files on my Nextcloud.

Example of my workflow

• searching/finding new research papers
• add them to my knowledge base
• read them, comment on them
• embed them in notes and write some text around it
• reference them in other notes

Requirements

• create notes and embed/link PDFs inside them, and being able to comment/highlight inside the PDFs
• preferably each note is a Markdown file and not part of a database, which could potentially corrupt (is that a thing?)
• being able to use Mathjax/Latex-Math expressions inside the markdown notes
• the PDFs can be cited/linked from other notes
• the notes and PDFs are shared or provided by a server and can be accessed by many different devices (Windows/Andoird/Linux) and maybe even via a web interface
• for books and journals I want the software to be able to fetch the metadata from online databases, and being able to generate the Bibtex snippet
• preferably the software is foss

What Ive already tried

I know the following softwares serve different purposes, but I had a look into them and tried, if they worked for me in the workflow I wanted. But nothing so far was a perfect fit and had minor or major annoyances.

Markdown Editors

• Obsidian (actually good, but some small things it really lacks, like relative linking outside the vault; and not foss)
• logseq
• Joplin

Wikis

• Bookstack (no native Mathjax and forced hierarchy)
• WikiJS
• Trilium (i like the PDF embed feature)

Citation Managers

• Citavi (and dont really like it, because its super old buggy)
• Zotero (actually very promising)

Others

• Calibre (I dont like their file naming with Kommata and Umlaute etc...)
• Kavita (focus is not so much on papers, more on just reading PDFs)

Not tried yet

• Komga
• Notion
• Roam Research
• Foam
• Dendron
• Capacities

Similar Posts

• https://www.reddit.com/r/selfhosted/comments/mo2h9i/searching_for_selfhosted_science_document/
• https://www.reddit.com/r/PKMS/comments/nfef59/list_of_personal_knowledge_management_systems/

Final Thoughts

Maybe the solution is a combination of the above mentioned software. Has anyone found a good way to realize the above mentioned workflow?

Any help is appreciated