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

  • @[email protected]BEnglish
    1•11 months ago

    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.