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
Anytype (ex Logseq and Obsidian user here)