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

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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