Deeppapernote
917Dhj/DeepPaperNote
Generate a high-quality deep-reading note for a single paper and write it into an Obsidian-style vault.
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.
Install Zotero Obsidian Bridge
$ npx skills add Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Galaxy-Dawn/claude-scholar 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/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .claude/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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/Galaxy-Dawn/claude-scholar/tree/main/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 Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Galaxy-Dawn/claude-scholar zotero-obsidian-bridge --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .agents/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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 Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Galaxy-Dawn/claude-scholar zotero-obsidian-bridge --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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/Galaxy-Dawn/claude-scholar.git --path 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 Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Galaxy-Dawn/claude-scholar 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/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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 Galaxy-Dawn/claude-scholar 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 Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .github/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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 Galaxy-Dawn/claude-scholar --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 Galaxy-Dawn/claude-scholar zotero-obsidian-bridge --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Galaxy-Dawn/claude-scholar.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/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/Galaxy-Dawn/claude-scholar/tree/main/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
- 5.7k
- Token cost
- ~514 tokens
- SKILL.md length
- 186 words
- Files
- 7 (incl. scripts, references)
- Skills in repo
- 34
- Repo updated
- First seen
- Licence
- MIT
At a glance
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.
- Turning a Zotero collection into linked notes in an Obsidian vault
- Runs Python scripts from its folder
- Keeping literature synthesis traceable to specific evidence records
- Deciding whether an abstract-only paper can support a claim in a report
What it does
The skill defines a flow from Zotero to Sources/Papers, then Knowledge, then Writing, then a Maps/literature.canvas graph. Each paper gets one canonical note under Sources/Papers, literature synthesis goes to Knowledge, writing-oriented output goes to Writing, and after a large ingestion the agent updates the system registry, the 02-Index file and the day's Daily note. Bundled files include a verify_paper_notes.py script, schemas for paper notes and collection inventories, a local Zotero fallback guide and a workflow reference.
Core papers and papers with reusable claims should carry an evidence record, while abstract-only or placeholder notes stay in To-Read until there is enough evidence. A Claim Promotion Gate blocks synthesis from landing in Knowledge or Writing unless every claim points to an evidence record ID, the source type is strong enough, and the wording limits are kept. Abstract-only and webpage placeholders cannot support durable claims.
When your agent uses it
- Turning a Zotero collection into linked notes in an Obsidian vault
- Keeping literature synthesis traceable to specific evidence records
- Deciding whether an abstract-only paper can support a claim in a report
- Auditing paper notes with the bundled verification script
Example prompts
- “Import the papers in my Zotero collection on retrieval into Sources/Papers in this vault.”
- “Write a literature synthesis in Knowledge that links back to each supporting paper note.”
- “Check which paper notes lack an evidence record before I draft the related work section.”
- “Run verify_paper_notes.py and tell me which notes fail the schema.”
Requirements
- A Zotero library as the source of papers
- An Obsidian project knowledge base with the expected folders
- Python to run verify_paper_notes.py
What it can do on your machine
Read from SKILL.md and the folder at commit 9037873. 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 514 tokens when it runs, and up to ~2.6k if it reads all its reference files. Until then it costs about 52 tokens; SKILL.md has 186 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
The full file from Galaxy-Dawn/claude-scholar at commit 9037873, republished under its MIT licence (© Galaxy-Dawn). 186 words, ~514 tokens.
Download SKILL.mdSave it as
.claude/skills/zotero-obsidian-bridge/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.- name
- zotero-obsidian-bridge
- description
- Use this skill when Zotero is the literature source of truth and the project KB should receive source notes under Sources/Papers plus project-linked synthesis in Knowledge and Writing.
- version
- 0.3.0
Zotero Obsidian Bridge
Use this skill when papers live in Zotero and the project KB should receive project-local notes.
Default flow:
Zotero -> Sources/Papers -> Knowledge -> Writing -> Maps/literature.canvasRules:
- one canonical paper note per paper under
Sources/Papers/ - literature synthesis goes to
Knowledge/ - writing-oriented outputs go to
Writing/ Maps/literature.canvasis the default derived graph artifact- update
_system/registry.md,02-Index.md, and today'sDaily/after substantial ingestion
Evidence extraction requirement
Core papers and papers with reusable claims should include an evidence record. Abstract-only or placeholder notes may stay in To-Read until there is enough evidence to extract a reusable claim.
## Evidence Record
Evidence ID:
Source:
Source type: full paper | preprint | dataset | experiment artifact | project note | abstract-only | webpage placeholder
Supports:
Contradicts:
Method / dataset / metric:
Limitation:
Project relevance:
Claim strength: speculative | observed | supported | strongUse ../research-ideation/references/research-contract.md as the shared contract for Evidence Records and claim strength definitions.
Before synthesis lands in Knowledge/ or Writing/, apply the shared Claim Promotion Gate:
- every promoted claim must point back to an Evidence Record ID,
- source type must be strong enough for the claim,
- abstract-only and webpage-placeholder items cannot support durable claims,
- allowed wording and forbidden stronger wording must be preserved when the claim may later enter a report, manuscript, or rebuttal.
When synthesis lands in Knowledge/, link the supporting paper notes explicitly. Do not promote literature synthesis that cannot point back to source notes.
© Galaxy-Dawn, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 6 other files (scripts, references) in skills/zotero-obsidian-bridge of Galaxy-Dawn/claude-scholar.
- 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 9037873
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 skillGalaxy-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 | |
| Comm Lit Review Claude SingleAI4Scientist/nano-scientist | 128 | 4 repos | ~2.2k | Automated safety check: Notes | None | |
| Obsidian Literature Workflowbrycewang-stanford/Auto-Empirical-Research-Skills | 4.6k | — | ~976 | Automated safety check: Pass | Custom licence |
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AI4Scientist/nano-scientist
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brycewang-stanford/Auto-Empirical-Research-Skills
A skill your agent uses when the user keeps paper notes inside an Obsidian project knowledge base and wants filesystem-first literature review, explicit agent-first Zotero ingestion, Papers/ plus…
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Analyzes arXiv papers, PDFs, project pages and blogs and writes an evidence-backed Obsidian note with images and a knowledge-graph entry.
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Related
Categories
Questions about Zotero Obsidian Bridge
What does Zotero Obsidian Bridge do?
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. canvas graph. Each paper gets one canonical note under Sources/Papers, literature synthesis goes to Knowledge, writing-oriented output goes to Writing, and after a large ingestion the agent updates the system registry, the 02-Index file and the day's Daily note.
When should I use Zotero Obsidian Bridge?
Zotero Obsidian Bridge fits situations like: turning a Zotero collection into linked notes in an Obsidian vault; keeping literature synthesis traceable to specific evidence records; deciding whether an abstract-only paper can support a claim in a report; auditing paper notes with the bundled verification script.
How do I install Zotero Obsidian Bridge in Claude Code?
Run `npx skills add Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a claude-code`. Or copy the skill folder (skills/zotero-obsidian-bridge in Galaxy-Dawn/claude-scholar) 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 Galaxy-Dawn/claude-scholar --skill zotero-obsidian-bridge -a codex`. Or copy the skill folder (skills/zotero-obsidian-bridge in Galaxy-Dawn/claude-scholar) 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 Galaxy-Dawn/claude-scholar --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: A Zotero library as the source of papers; An Obsidian project knowledge base with the expected folders; Python to run verify_paper_notes.py.
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 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 Obsidian Bridge use?
About 514 tokens (SKILL.md is roughly 2.1k 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 2.1k 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: Deeppapernote (917Dhj/DeepPaperNote, 1.2k stars), Zotero Taxonomy Curator (ganzoth/zotero-taxonomy-curator, 160 stars), Obsidian Paper Vault (Aperivue/medsci-skills, 333 stars) and Comm Lit Review Claude Single (AI4Scientist/nano-scientist, 128 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?
Galaxy-Dawn (a GitHub user) maintains it in Galaxy-Dawn/claude-scholar, which has 5,725 GitHub stars. The repository holds 34 skills in this directory. The repository was last updated on September 23, 2026.
Source: Galaxy-Dawn/claude-scholar on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.