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

  • nklsBEnglish
    1·
    1 year ago

    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.

    ​

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