Looking for a Personal Research Management Tool reddit / selfhosted ---------------------------------------------------------------------- julianmueller2211 · 2023-10-22 12:19 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 ## Similar Posts - https://www.reddit.com/r/selfhosted/comments/mo2h9i/searching_for_se lfhosted_science_document/ - https://www.reddit.com/r/PKMS/comments/nfef59/list_of_personal_knowl edge_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 ---------------------------------------------------------------------- TheDeepTech · 2023-10-22 14:19 The plural form of software is also software. ---------------------------------------------------------------------- emprahsFury · 2023-10-22 14:29 Or, when OP is talking about nested plurals 'softwares' makes sense. If we're talking about groups of tuna and groups of mackerel- fishes makes sense. Same thing. ---------------------------------------------------------------------- nkls · 2023-10-22 15:14 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](https://www.zotero.org/support/note_templates) 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! ---------------------------------------------------------------------- JoeB- · 2023-10-22 15:16 I use **Joplin** every day for taking my own technical notes, often with screenshots. I use it across multiple devices and operating systems that sync through Dropbox. Notes are exported to PDF when there is a need to share them, which is infrequent. **Zotero** looks keenly focused on managing research information and creating bibliographies. I am not actively involved in research, but I just downloaded and installed it on my M1 MacBook Air out of curiosity. I opened the Zotero app, tried to create a new folder, and it immediately froze. It also looked outdated. Hope you have better luck with it. ---------------------------------------------------------------------- MrSupremo · 2023-10-22 16:24 I use zotero with logseq and synchronize everything between my devices using syncthing. It's all pretty easy to set up with little research, I think. Logseq has a good integration with zotero and lets you annotate pdfs directly in it (although the notes stay in logseq, not on the Pdf). It's also good to link themes and topics with certain papers (e.g., papers on accessibility). I find it pretty easy to find papers like that. Some plugins help "make it yours". But I can't link to them now. ---------------------------------------------------------------------- igderkoman · 2023-10-22 16:58 There is no fishes and no softwares ever. Unless English isn’t your native. ---------------------------------------------------------------------- Delicious_Dust8068 · 2023-10-22 17:05 You're going to lose your mind when you find about grammar. https://www.grammarly.com/blog/fish-fishes/ ---------------------------------------------------------------------- IceOleg · 2023-10-22 19:23 Its a bit of work to get into it, but Emacs Org mode with org-roam, combined with Zotero + Better BibTeX plugin works really well for me. ---------------------------------------------------------------------- austozi · 2023-10-22 20:05 [Zotero](https://www.zotero.org), 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](https://github.com/mkucej/i-librarian-free) 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. ---------------------------------------------------------------------- chaplin2 · 2023-10-22 21:17 Is paperless-ngx useful for this too? ---------------------------------------------------------------------- gr8dude · 2023-10-23 07:58 I've been a happy Zotero user for 6+ years, I strongly recommend it. ---------------------------------------------------------------------- fvnjk · 2023-10-23 09:51 Hi, I am actually currently in the process of starting a startup/product that develops something like this. Totally haven't thought about making a self-hosted version, but that could definitely be an option! If anyone would like to help us out and fill in our survey where we identify the key frustrations that people have, here is the link: [htt ps://tally.so/r/wMN2Wl](https://tally.so/r/wMN2Wl?utm_source=reddit&ut m_campaign=international&utm_content=comment) It would help us a lot, and hopefully, we'll be able to offer a useful product based on this soon! ---------------------------------------------------------------------- julianmueller2211 · 2023-10-30 07:30 I also use paperless for organising documents (like postal stuff), but they clearly state in their wiki, that paperless is not meant for organising research papers, although the OCR is neat. But Commenting etc is not really wrking in there. But thanks for mentioning! ---------------------------------------------------------------------- julianmueller2211 · 2023-10-30 07:43 I participated in your survey. Id like to know more about this, maybe you can dm me? ---------------------------------------------------------------------- julianmueller2211 · 2023-10-30 07:45 I setteled on this solution! Thanks :) One plugin I use is "Zotfile", which lets me sync my zotero entries to a pdf in relative path. All files live on my nextcloud and therefore are accessible and sync across all my devices. Next, I need to get Obsidian to work with relative paths outside the vault, which is an entirely different problem... ---------------------------------------------------------------------- fvnjk · 2023-10-30 08:00 Dmed! ---------------------------------------------------------------------- stevenslibby · 2023-11-14 22:01 Here are two short comments about https://legalpdf.io in response to the post: "legalpdf.io looks like it could be a handy tool to help organize and annotate research papers efficiently. The AI-powered features for legal research and document drafting seem like they could save a lot of time." "I like how quickly legalpdf.io can scan and pull key information from legal documents. Its AI research assistant seems like it would be useful for compiling case law and citations.