Zotero Obsidian Bridge
Galaxy-Dawn/claude-scholar
Moves papers from Zotero into an Obsidian project knowledge base as source notes, literature synthesis and writing outputs, with evidence records behind every promoted claim.
Sync Zotero references to Obsidian and Logseq markdown. An agent skill from wentorai/research-plugins.
Install Zotero Markdb Connect Guide
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guide --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .claude/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .claude/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guideType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .agents/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .agents/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .cursor/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .cursor/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/tools/knowledge-graph/zotero-markdb-connect-guide--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .gemini/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .gemini/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guideInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .github/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .github/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins zotero-markdb-connect-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/tools/knowledge-graph/zotero-markdb-connect-guide .opencode/skills/zotero-markdb-connect-guide && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "zotero-markdb-connect-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/tools/knowledge-graph/zotero-markdb-connect-guide into .opencode/skills/zotero-markdb-connect-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-markdb-connect-guide", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
zotero-markdb-connect-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~1k tokens
- SKILL.md length
- 102 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Sync Zotero references to Obsidian and Logseq markdown. An agent skill from wentorai/research-plugins.
- Works in 5 steps: Literature management: Seamless Zotero ↔… → Knowledge building: Link papers to… → Annotation workflow: PDF annotations in… → …
- Tasks that involve Citation management
- SKILL.md covers Overview, Installation, Configuration and Note Template, plus 5 more sections
- Reaches doi.org
What it does
Zotero Markdb Connect Guide is an agent skill from wentorai/research-plugins. Sync Zotero references to Obsidian and Logseq markdown
Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Citation management. It works with Zotero and Obsidian. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Citation management
Example prompts
- “/zotero-markdb-connect-guide”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Literature management: Seamless Zotero ↔ Obsidian workflow
- Knowledge building: Link papers to concept notes
- Annotation workflow: PDF annotations in Markdown
- Research writing: Quick access to notes while writing
- Zettelkasten: Literature notes as part of note network
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown and bash).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
doi.org
Also links to:
github.comobsidian.mdlogseq.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Zotero Markdb Connect Guide loads about 1k tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 102 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 102 words, ~1,011 tokens.
Download SKILL.mdSave it as
.claude/skills/zotero-markdb-connect-guide/SKILL.md (or your agent's skills folder).- name
- zotero-markdb-connect-guide
- description
- Sync Zotero references to Obsidian and Logseq markdown
Zotero MarkDB-Connect Guide
Overview
Zotero MarkDB-Connect bridges Zotero with Markdown-based knowledge management tools (Obsidian, Logseq). It creates and maintains bidirectional links between Zotero items and their corresponding Markdown literature notes, enabling seamless navigation between your reference manager and PKM system. Syncs metadata, annotations, and tags.
Installation
# Download .xpi from GitHub releases
# Zotero 7: Tools → Add-ons → Install Add-on From FileConfiguration
### Settings (Edit → Preferences → MarkDB-Connect)
**Markdown Vault Path:**
- Point to your Obsidian vault or Logseq directory
- Example: ~/Documents/ObsidianVault/Literature/
**Note Template:**
- Customize the Markdown template for new literature notes
- Uses Zotero item fields as variables
**Sync Options:**
- Auto-create notes for new items
- Sync annotations to Markdown
- Bidirectional tag sync
- Update existing notes on item changeNote Template
<!-- Template for literature notes -->
---
title: "{{title}}"
authors: [{{authors}}]
year: {{year}}
doi: {{doi}}
citekey: {{citekey}}
tags: [{{tags}}]
zotero: {{zoteroSelectURI}}
---
# {{title}}
**Authors:** {{authors}}
**Year:** {{year}}
**Venue:** {{publicationTitle}}
**DOI:** [{{doi}}](https://doi.org/{{doi}})
## Abstract
{{abstractNote}}
## Annotations
{{annotations}}
## Key Takeaways
-
## Notes
-
## Connections
- Related: [[]]
- Builds on: [[]]
- Contradicts: [[]]Obsidian Integration
### Folder Structure
ObsidianVault/
├── Literature/ # Auto-generated literature notes
│ ├── vaswani2017.md
│ ├── devlin2019.md
│ └── brown2020.md
├── Concepts/ # Your concept notes
│ ├── Attention.md # Links to [[vaswani2017]]
│ └── Pre-training.md # Links to [[devlin2019]]
└── Projects/ # Project notes referencing papers
### Workflow
1. Import paper in Zotero (via browser connector)
2. MarkDB-Connect auto-creates Literature/citekey.md
3. In Obsidian: open literature note, add your thoughts
4. Link to concept notes using [[wikilinks]]
5. Annotations sync from Zotero PDF readerAnnotation Sync
### Zotero PDF Annotations → Markdown
When you highlight or annotate in Zotero's PDF reader:
> [!quote] Highlight (Yellow)
> "The attention mechanism allows focusing on relevant parts"
> — p. 3
> [!note] Note
> This is the key insight — attention replaces recurrence
> — p. 3, linked to highlight above
> [!important] Red Highlight
> "Our model achieves 28.4 BLEU on WMT 2014"
> — p. 7
Annotations auto-sync to the Markdown note when updated.Logseq Integration
### Logseq-Specific Setup
- Set vault path to your Logseq pages directory
- Notes created as Logseq pages with properties block
- Uses Logseq property syntax instead of YAML frontmatter
### Logseq Note Format
title:: Attention Is All You Need
authors:: [[Vaswani]], [[Shazeer]]
year:: 2017
doi:: 10.48550/arXiv.1706.03762
tags:: #transformer #attention
zotero:: zotero://select/items/...
- Key contributions
- Self-attention mechanism replacing recurrence
- Multi-head attention for different representation subspacesUse Cases
- Literature management: Seamless Zotero ↔ Obsidian workflow
- Knowledge building: Link papers to concept notes
- Annotation workflow: PDF annotations in Markdown
- Research writing: Quick access to notes while writing
- Zettelkasten: Literature notes as part of note network
References
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/tools/knowledge-graph/zotero-markdb-connect-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Zotero Markdb Connect Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Zotero Markdb Connect Guide this skillwentorai/research-plugins | 298 | 1 repos | ~1k | Automated safety check: Pass | MIT | |
| Zotero Obsidian BridgeGalaxy-Dawn/claude-scholar | 5.7k | — | ~514 | Automated safety check: Pass | MIT | |
| Deeppapernote917Dhj/DeepPaperNote | 1.2k | 1 repos | ~5.9k | Automated safety check: Pass | MIT | |
| Zotero Taxonomy Curatorganzoth/zotero-taxonomy-curator | 160 | — | ~2.3k | Automated safety check: Pass | MIT | |
| Obsidian Paper VaultAperivue/medsci-skills | 333 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Lit SyncAperivue/medsci-skills | 333 | — | ~4.6k | Automated safety check: Pass | MIT |
Similar skills
Deeppapernote
917Dhj/DeepPaperNote
Generate a high-quality deep-reading note for a single paper and write it into an Obsidian-style vault.
Zotero Taxonomy Curator
ganzoth/zotero-taxonomy-curator
Domain-configurable Zotero-to-Obsidian literature curation and paper close-reading skill.
Obsidian Paper Vault
Aperivue/medsci-skills
A skill your agent uses when turning a folder of research PDFs into Obsidian notes, even if Obsidian is not named.
Lit Sync
Aperivue/medsci-skills
A skill your agent uses when references in a .bib file (often from /search-lit) should land in Zotero and Obsidian.
Zotlit Citations
aidenlx/zotlit
Answer citation questions about an Obsidian vault through ZotLit: which notes cite a work, what a document cites, and why a citation is broken.
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Related
Categories
Questions about Zotero Markdb Connect Guide
What does Zotero Markdb Connect Guide do?
Sync Zotero references to Obsidian and Logseq markdown. An agent skill from wentorai/research-plugins. Zotero Markdb Connect Guide is an agent skill from wentorai/research-plugins.
When should I use Zotero Markdb Connect Guide?
Zotero Markdb Connect Guide fits situations like: tasks that involve Citation management.
How do I install Zotero Markdb Connect Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a claude-code`. Or copy the skill folder (skills/tools/knowledge-graph/zotero-markdb-connect-guide in wentorai/research-plugins) into .claude/skills/zotero-markdb-connect-guide in your project. Claude Code loads it when a task matches its description.
How do I install Zotero Markdb Connect Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a codex`. Or copy the skill folder (skills/tools/knowledge-graph/zotero-markdb-connect-guide in wentorai/research-plugins) into .agents/skills/zotero-markdb-connect-guide in your project. Codex loads it when a task matches its description.
Can I use Zotero Markdb Connect Guide in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill zotero-markdb-connect-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/zotero-markdb-connect-guide, .gemini/skills/zotero-markdb-connect-guide, .github/skills/zotero-markdb-connect-guide and .opencode/skills/zotero-markdb-connect-guide in your project.
What does Zotero Markdb Connect Guide need to run?
SKILL.md names no scripts, command-line tools or credentials: Zotero Markdb Connect Guide is instructions for the agent only.
Does Zotero Markdb Connect Guide access the network?
SKILL.md names 4 domains. In commands or code: doi.org; the agent is likely to contact it when it follows the instructions. As links in the text: github.com, obsidian.md and logseq.com. This is read from the text; nothing was executed.
Is Zotero Markdb Connect Guide safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Zotero Markdb Connect Guide use?
Zotero Markdb Connect Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Zotero Markdb Connect Guide use?
About 1k tokens (SKILL.md is roughly 4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Zotero Markdb Connect Guide?
Skills that share tags, products or a category with Zotero Markdb Connect Guide: Zotero Obsidian Bridge (Galaxy-Dawn/claude-scholar, 5.7k stars), Deeppapernote (917Dhj/DeepPaperNote, 1.2k stars), Zotero Taxonomy Curator (ganzoth/zotero-taxonomy-curator, 160 stars) and Obsidian Paper Vault (Aperivue/medsci-skills, 333 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Zotero Markdb Connect Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.