r/zotero

Ask questions across your Markdown notes using a fully local Graph RAG engine. Built for Obsidian vaults, works with any folder of Markdown files. Extracts entity-relation triples from wikilinks & YAML frontmatter, retrieves answers via hybrid search (vector + BM25 + temporal). Multilingual. No cloud. Runs on Ollama.

https://github.com/benmaster82/Kwipu

Hey folks! Just popping in the share a (pre) weekend open-source project…

I’ve been working with larger libraries (10k+ records) recently and have ended up rolling my own Zotero sync + full text search solution backed by Cloudflare. It gets you 10GB of cloud storage for free (under $20/mo for 1TB of PDFs) & exposes a remote MCP so Claude can actually use your library as a source in research mode.

All ive done is host a thin WebDAV <> S3 server using my homelab and tailscale. Then, on the same machine, I have a worker that ingests new PDFs (md conversion -> chunks -> embedding) and stores the vectors back in the same bucket with LanceDB.

Put a remote MCP server on there too which then you can use to connect the whole thing to Claude. Since, it’s a remote MCP server, the research mode can actually use it as a source. See attached picture.

Repo link: https://github.com/ElliotRoe/lit-bucket

Hi everyone,

It’s been a while since we last posted here.

About 7 months ago, we shared an early version of DeepTutor with the Zotero community. We got 200+ pieces of feedback from people here, and honestly, a lot of it shaped what we worked on next. Thank you to everyone who tried it, left comments, or kept sending us suggestions after the post.

Since then, DeepTutor has grown to 4,000+ users. Our team has been focused on making it fit better into real research workflows by listening closely to what researchers actually need.

DeepTutor started with PDF chat, but that is only one part of how people work with papers. In practice, you often need to move between papers, find a section you read months ago, check related work, translate part of a paper, or look at the code behind a project.

So the biggest update is auto context across your Zotero library. Whether your library has hundreds or thousands of files, instead of manually picking the right paper first, you can ask a broader question, and DeepTutor will try to find the relevant papers, files, and sections from your Zotero library. It also shows source highlights, so you can check where the answer is coming from.

We’ve also added arXiv search, auto-tagging, in-reader paper translation, code and notebook support, and links from papers to related GitHub repos.

DeepTutor is free to try. We also have a referral program that gives one free month of Pro.

You can try it here: https://deeptutor.knowhiz.us

We’d really appreciate feedback from Zotero users. Feel free to leave any comments! We’ll read and respond.

Sharing something we built that leans heavily on Zotero, in case it's useful to anyone here.

Some background: part of our work involves ontologies — the big structured vocabularies behind biomedical and knowledge-graph data. Every claim in one is supposed to be backed by a real source, and matching those sources by hand is miserable. So we built Sci2Code, which uses your Zotero library as the source of truth:

• Search your Zotero library from inside VSCode — type "heart", get your matching references instantly
• Insert a proper, DOI-backed citation into the data with one click — author, year, journal, DOI all pulled through
• Flags anything with no DOI and prompts you to add one, so you're not silently citing unverifiable sources

Basically it turns Zotero into the citation backbone for structured data instead of just a bibliography for a paper.

It's free and open source — repo's in the comments so you can see exactly what it does with your library. It's part of a larger ontology editor we're building, but the Zotero piece stands on its own.

Mostly posting to sanity-check the workflow: for those of you who use Zotero as a serious research backbone, does pulling citations out of Zotero into other tools like this match how you work? What would you want it to do?

Hi everyone,

As a researcher, when I am trying to write my articles, I see myself spending way too much time going back and forth between my Zotero library and Microsoft Word. But I find myseld there is this repetitive task of constant copying, pasting, and manual formatting of text, tables, and headings. Sometimes when doing all these tasks, I tend to forget what the original idea was. So I decided to stitch together a solution as a hobby project.

Right now, I am working on a setup using a Word plugin that talks to a local LLM running completely offline on my machine. To avoid the hallucination problem, I hooked it up to the Zotseek plugin to pull context directly from my Zotero library via the API. It uses semantic search to grab the exact facts from my indexed articles, so the AI actually sticks to the data in my library. As a bonus, the Word plugin automatically parses the markdown output from the LLM and formats it directly into native Word styles, like proper headings, tables, and equations, without me needing to click around.

I am now working on automated references so that the context pulled from my Zotero library can be inserted directly into the LLM-generated content at the relevant positions, following specific citation styles like APA or IEEE. After that, the bibliography can be generated at the end on demand, linked directly to those inserted citations. Once this feature is implemented, my tool will be complete.

So far, the tool is doing exactly what I need: it retrieves the right information from my Zotero library, pulls it into Word, and formats it so I can immediately build out the draft. I don't see it as a full-fledged writing assistant since it is still in a very preliminary stage. But before I go any further with cleaning up the code or adding features, I wanted to ask: does something like this already exist for Word? I could not find a local RAG tool specifically for a Zotero library that behaves like this inside Word, but I might have missed it.

+-----------------------------------------------------+
|                  MS Word Plugin                     |
+-----------------------------------------------------+
   |                                               ^
   | (User Prompt)                                 | (Auto-Parse Markdown
   v                                               |  & Insert Citations)
+-------------------+                              |
|  Zotseek Plugin   |                              |
+-------------------+                              |
   |                                               |
   | (Semantic Search                              |
   |  on Zotero Library)                           |
   v                                               |
+-------------------+                              |
|   Local AI LLM    | -----------------------------+
+-------------------+
   |
   | (On-Demand Bibliography)
   v
+-------------------+
|   Bibliography    |
| (Linked to Style) |
+-------------------+

If it doesn't exist, would anyone else find a tool like this useful?

Zotero Watch Folder watches a folder you choose and imports whatever lands in it:

What it does:

- Auto-import with metadata. New PDFs (in the folder and subfolders) are imported and run through Zotero's recognizer. If that comes up empty, a fallback reads page 1 for a single clean DOI/arXiv/ISBN and looks it up; failing that it makes a filename-titled placeholder tagged _needs-review, so nothing lands as a nameless orphan.

- Real dedup. Files are matched by full-content hash (drop the same paper twice, even renamed, and you get one item), and the fingerprint is stamped into each item so dedup survives a reinstall or a wiped database. Optional DOI/ISBN/fuzzy-title matching and template renaming too.

- You choose where the PDF lives: stored in Zotero (works with WebDAV like pCloud), linked from the watch folder to save Zotero storage, or both. Includes a tool to convert stored PDFs to linked ones to reclaim space.

- Optional library mirror. Your collections become a folder tree on disk (nested collections nest, unfiled items sit at the root, virtual views like Trash/Duplicates are skipped). Rename a collection in Zotero and the folder follows. A plain-files copy of your library you can browse or back up.

- Deletion sync is opt-in and heavily guarded. Off by default. When enabled, removals go to a recoverable trash (not permanent), nothing is deleted unless a fresh hash proves the file is unchanged, and it pauses instead of mass-deleting if a cloud folder or drive briefly drops out. The whole delete path is fail-closed: anything uncertain keeps your file.

One caution: this can move and (if you opt in) trash files, so back up your Zotero database and storage folder first. I would start with plain import mode before turning on the mirror or delete features.

Still fairly new, so I would value feedback from daily Zotero users: what breaks, what is confusing, and whether the import or the mirror is the part you would actually use.

It works on Zotero 7, 8, and 9 (tested on 9.0.4), is GPL-3.0, and installed copies auto-update.

Repo (install + docs): https://github.com/josesiqueira/zotero-watch-folder

Hello all! I'm writing to you from the University of Connecticut to share our new project developed in collaboration with Digital Scholar, the same non-profit behind Omeka & Zotero: Sourcery.

Sourcery connects researchers with archive users in more than 50 U.S. cities who provide reference-quality scans of archival materials. Request materials from multiple repositories to explore new collections or collect critical documents, no travel required.

I think you folks might be interested in becoming a Sourcerer to earn extra money creating scans for other researchers. You can fulfill Sourcery jobs and advance your skills while exploring institutions and collections on your own schedule.

Payment includes a base retrieval pay of $22.50, which you would receive regardless of the size or type of request. You would also receive this payment if the materials are unable to be scanned for whatever reason (missing, for example). You would also get paid $0.27 per scan returned to the requester with a max of 400 scans.

As mentioned, Sourcery is currently available in over 50 U.S. cities (we're not international yet, but working on it!). You can view our current locations at https://sourceryapp.org/locations/. If you'd like to sign-up to complete requests but your location isn't available, shoot us an email at sourceryapp[at]gmail.com and we can meet with you and chat about making your city available.

Sourcery is produced by Digital Scholar and the University of Connecticut, with funding from the Mellon Foundation. Learn more at sourceryapp.org.

Happy to answer any questions!

I made this a while back and use it so much so wanted to share it.

https://github.com/Acatechnic/zotero-scholar-search

Adds options in the right-click menu to search selected text from a pdf. By default, it searches Google Scholar but you can add/customise both the search engine and the browser to your liking. Trying to keep it simple but let me know what works or doesn't!

It's really helped my ADHD brain get to new sources without having to be distracted by manually opening a browser etc.

hope it helps!

Acatechnic :)

I made a plugin called Grounded Q&A that lets you ask questions about the papers in your Zotero library and get answers that link straight back to the exact page in the source PDF. Every claim is cited and clickable, so you can verify it instead of trusting a black-box summary.

It works on a single paper or across many at once, and it's bring-your-own-model — you can plug in Claude, GPT, Ollama (fully local), DeepSeek, or Grok, so you control cost and privacy.

It's free and open source. I'd really value feedback from people who live in Zotero daily — what breaks, what's missing, what would make it part of your workflow.

Repo: https://github.com/birugit/zotero-grounded-qa