Annotate Paper
54yyyu/zotero-mcp
Read the open paper and write study annotations into its PDF with zotero-cli - a context box on the title, a four-part summary on the abstract, role-coded abstract highlights, one box per figure…
Agent skill
Zotero Obsidian Bridge
by brycewang-stanford in brycewang-stanford/Auto-Empirical-Research-Skills
A skill your agent uses when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a…
Install Zotero Obsidian Bridge
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridge --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/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .claude/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .claude/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridgeType 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridge --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .agents/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .agents/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridge --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .cursor/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .cursor/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge--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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridge --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .gemini/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .gemini/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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 brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridgeInstalls 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .github/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .github/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills zotero-obsidian-bridge --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge .opencode/skills/zotero-obsidian-bridge && 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-obsidian-bridge" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge into .opencode/skills/zotero-obsidian-bridge/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "zotero-obsidian-bridge", 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-obsidian-bridge- GitHub stars
- 4.6k
- Token cost
- ~1.5k tokens
- SKILL.md length
- 681 words
- Files
- 7 (incl. scripts, references)
- Skills in repo
- 383
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
A skill your agent uses when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a…
- Works in 10 steps: Resolve the current project via… → Read Zotero items from the target… → For each paper → …
- Papers are collected in Zotero but the user wants detailed reading notes
- SKILL.md covers Core stance, Default workflow, Default outputs and Safety rules, plus 1 more section
- Runs Python scripts from its folder
What it does
Zotero Obsidian Bridge is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Use this skill when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a connected knowledge map inside the bound Obsidian project knowledge base.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including scripts and reference files (for example `examples/example-collection-inventory.md`, `references/COLLECTION-INVENTORY-SCHEMA.md` and `references/LOCAL-ZOTERO-FALLBACK.md`).
It sits in Research & Science, covering Citation management. It works with Zotero, Obsidian and Model Context Protocol. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…
When your agent uses it
- Papers are collected in Zotero but the user wants detailed reading notes
- Project-linked literature synthesis
- Collection-wide paper-note coverage checks
- A connected knowledge map inside the bound Obsidian project knowledge base
Example prompts
- “/zotero-obsidian-bridge”
Requirements
- Python 3
Workflow steps
10 steps, taken from the first numbered list in SKILL.md.
- Resolve the current project via $obsidian-project-memory.
- Read Zotero items from the target collection/query.
- For each paper
- Add project-facing structure to each paper note
- Synthesize the batch into durable Knowledge/ notes such as
- If the request is collection-scoped, update a durable inventory note that records
- Refresh Maps/literature.canvas.
- If the user also wants writing deliverables, update
- Update today's Daily/ note and repo-local project memory.
- Run a deterministic verification pass after batch ingestion or schema refactors.
What it can do on your machine
Read from SKILL.md and the folder at commit 9fa87d8. 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
Ships 1 file in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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 Obsidian Bridge loads about 1.5k tokens when it runs, and up to ~3.3k if it reads all its reference files. Until then it costs about 69 tokens; SKILL.md has 681 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); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 681 words (~1,497 tokens).
“Bridge Zotero as the literature source of truth with Obsidian as the durable project knowledge base.”
- name
- zotero-obsidian-bridge
- version
- 0.2.0
Files
SKILL.md and 6 other files (scripts, references) in skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge of brycewang-stanford/Auto-Empirical-Research-Skills.
- SKILL.md
- examples/example-collection-inventory.md
- references/COLLECTION-INVENTORY-SCHEMA.md
- references/LOCAL-ZOTERO-FALLBACK.md
- references/PAPER-NOTE-SCHEMA.md
- references/WORKFLOW.md
- scripts/verify_paper_notes.py
Open the folder on GitHubat commit 9fa87d8
Compare with similar skills
Zotero Obsidian Bridge 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 Obsidian Bridge this skillbrycewang-stanford/Auto-Empirical-Research-Skills | 4.6k | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Annotate Paper54yyyu/zotero-mcp | 5.3k | — | ~1.5k | Automated safety check: Pass | MIT | |
| Deeppapernote917Dhj/DeepPaperNote | 1.2k | 1 repos | ~5.9k | Automated safety check: Pass | MIT | |
| NSFC Literature Review WriterHuiyuLi-2000/Chinese-Grant-Writer-Skills | 439 | 1 repos | ~1.4k | Automated safety check: Notes | 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 |
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Deeppapernote
917Dhj/DeepPaperNote
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NSFC Literature Review Writer
HuiyuLi-2000/Chinese-Grant-Writer-Skills
Writes the research-status literature review and critique section of an NSFC grant proposal, backed by a bundled multi-source literature search.
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.
CLI Anything Zotero
PiaoyangGuohai1/cli-anything-zotero
Full-featured CLI for Zotero reference management. An agent skill from PiaoyangGuohai1/cli-anything-zotero.
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Related
Works with
Categories
Questions about Zotero Obsidian Bridge
What does Zotero Obsidian Bridge do?
A skill your agent uses when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a…. Zotero Obsidian Bridge is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Use this skill when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a connected knowledge map inside the bound Obsidian project knowledge base.
When should I use Zotero Obsidian Bridge?
Zotero Obsidian Bridge fits situations like: papers are collected in Zotero but the user wants detailed reading notes; project-linked literature synthesis; collection-wide paper-note coverage checks; A connected knowledge map inside the bound Obsidian project knowledge base.
How do I install Zotero Obsidian Bridge in Claude Code?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a claude-code`. Or copy the skill folder (skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/zotero-obsidian-bridge in your project. Claude Code loads it when a task matches its description.
How do I install Zotero Obsidian Bridge in Codex?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -a codex`. Or copy the skill folder (skills/33-Galaxy-Dawn-claude-scholar/skills/zotero-obsidian-bridge in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/zotero-obsidian-bridge in your project. Codex loads it when a task matches its description.
Can I use Zotero Obsidian Bridge 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill zotero-obsidian-bridge -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-obsidian-bridge, .gemini/skills/zotero-obsidian-bridge, .github/skills/zotero-obsidian-bridge and .opencode/skills/zotero-obsidian-bridge in your project.
What does Zotero Obsidian Bridge need to run?
Going by SKILL.md and its folder, Zotero Obsidian Bridge needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Zotero Obsidian Bridge access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Zotero Obsidian Bridge 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Zotero Obsidian Bridge use?
Zotero Obsidian Bridge has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Zotero Obsidian Bridge use?
About 1.5k tokens (SKILL.md is roughly 6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.8k tokens, read only when the agent opens those files.
What are the alternatives to Zotero Obsidian Bridge?
Skills that share tags, products or a category with Zotero Obsidian Bridge: Annotate Paper (54yyyu/zotero-mcp, 5.3k stars), Deeppapernote (917Dhj/DeepPaperNote, 1.2k stars), NSFC Literature Review Writer (HuiyuLi-2000/Chinese-Grant-Writer-Skills, 439 stars) and Zotero Taxonomy Curator (ganzoth/zotero-taxonomy-curator, 160 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Zotero Obsidian Bridge?
brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,556 GitHub stars. The repository holds 383 skills in this directory. The repository was last updated on October 5, 2026.
Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.