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.
Reference manager with PDF viewer and Markdown note support. An agent skill from wentorai/research-plugins.
Install Sophosia Reference Guide
$ npx skills add wentorai/research-plugins --skill sophosia-reference-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins sophosia-reference-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/literature/metadata/sophosia-reference-guide .claude/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .claude/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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/literature/metadata/sophosia-reference-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 sophosia-reference-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins sophosia-reference-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/literature/metadata/sophosia-reference-guide .agents/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .agents/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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 sophosia-reference-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins sophosia-reference-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/literature/metadata/sophosia-reference-guide .cursor/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .cursor/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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/literature/metadata/sophosia-reference-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 sophosia-reference-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins sophosia-reference-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/literature/metadata/sophosia-reference-guide .gemini/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .gemini/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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 sophosia-reference-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 sophosia-reference-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/literature/metadata/sophosia-reference-guide .github/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .github/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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 sophosia-reference-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 sophosia-reference-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/literature/metadata/sophosia-reference-guide .opencode/skills/sophosia-reference-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 "sophosia-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/metadata/sophosia-reference-guide into .opencode/skills/sophosia-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sophosia-reference-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
sophosia-reference-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~810 tokens
- SKILL.md length
- 108 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Reference manager with PDF viewer and Markdown note support. An agent skill from wentorai/research-plugins.
- Works in 5 steps: Reading workflow: PDF + notes in single… → Visual thinking: Excalidraw diagrams… → Literature review: Linked notes across… → …
- Tasks that involve Note-taking
- SKILL.md covers Overview, Installation, Features and Workspace Structure, plus 4 more sections
- Calls npm and git; reaches github.com
What it does
Sophosia Reference Guide is an agent skill from wentorai/research-plugins. Reference manager with PDF viewer and Markdown note support
Its SKILL.md is about 810 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 Knowledge Management, covering Note-taking, Citation management and PDF. It works with Excalidraw. 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 Note-taking
- Tasks that involve Citation management
- Tasks that involve PDF
Example prompts
- “/sophosia-reference-guide”
Requirements
- Node.js
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Reading workflow: PDF + notes in single workspace
- Visual thinking: Excalidraw diagrams alongside papers
- Literature review: Linked notes across paper collection
- Presentation prep: Visual notes exportable as diagrams
- Research journal: Rich per-paper documentation
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
Shell commands in SKILL.md call:
npmgit
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:
github.com
Also links to:
excalidraw.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
Sophosia Reference Guide loads about 810 tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 108 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). 108 words, ~810 tokens.
Download SKILL.mdSave it as
.claude/skills/sophosia-reference-guide/SKILL.md (or your agent's skills folder).- name
- sophosia-reference-guide
- description
- Reference manager with PDF viewer and Markdown note support
Sophosia Reference Manager Guide
Overview
Sophosia is an open-source reference manager that combines PDF viewing, Markdown note-taking, and Excalidraw visual notes in a single application. Unlike traditional reference managers, it treats each paper as a rich workspace with typed annotations, linked notes, and visual diagrams. Built with modern web technologies (Electron + Vue), it runs on all desktop platforms.
Installation
# Download from GitHub releases (Windows/macOS/Linux)
# Or build from source:
git clone https://github.com/sophosia/sophosia.git
cd sophosia
npm install && npm run buildFeatures
### Core Capabilities
- **PDF Viewer**: Built-in reader with annotations
- **Markdown Notes**: Rich note editor per paper
- **Excalidraw**: Visual whiteboard for diagrams
- **Tags & Collections**: Flexible organization
- **BibTeX Support**: Import/export bibliography
- **Full-text Search**: Search across all papers
- **Citation Graph**: Visual paper relationships
### Note Types
1. **Text notes** — Markdown with LaTeX math
2. **Visual notes** — Excalidraw canvas
3. **Annotation notes** — Linked to PDF highlights
4. **Outline notes** — Structured paper summariesWorkspace Structure
### Per-Paper Workspace
Paper: "Attention Is All You Need"
├── PDF (with highlights and annotations)
├── Notes/
│ ├── summary.md (structured summary)
│ ├── ideas.md (research ideas sparked)
│ └── architecture.excalidraw (visual diagram)
├── Metadata (title, authors, year, DOI, tags)
└── Links (related papers, concept connections)Note-Taking Features
### Markdown Notes Support
- Standard Markdown formatting
- LaTeX math: $E = mc^2$ and display equations
- Code blocks with syntax highlighting
- Tables and checklists
- Wikilinks: [[other-paper]] for cross-referencing
- Embeds: ![[figure.png]] for inline images
- Templates for consistent note structure
### Excalidraw Integration
- Draw architecture diagrams
- Mind maps for paper concepts
- Comparison charts between methods
- Hand-drawn style for informal notes
- Export as SVG/PNG for presentationsImport/Export
### Import Sources
- BibTeX (.bib)
- RIS format
- DOI lookup (auto-fetch metadata)
- PDF drag-and-drop (auto-extract metadata)
- Zotero export files
### Export Formats
- BibTeX for LaTeX
- Markdown bibliography
- CSV metadata export
- HTML reading listsUse Cases
- Reading workflow: PDF + notes in single workspace
- Visual thinking: Excalidraw diagrams alongside papers
- Literature review: Linked notes across paper collection
- Presentation prep: Visual notes exportable as diagrams
- Research journal: Rich per-paper documentation
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/literature/metadata/sophosia-reference-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
Sophosia Reference 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 |
|---|---|---|---|---|---|---|
| Sophosia Reference Guide this skillwentorai/research-plugins | 298 | 1 repos | ~810 | Automated safety check: Pass | MIT | |
| Obsidian Paper VaultAperivue/medsci-skills | 333 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Ref Downloaderltczding-gif/ref-downloader | 139 | — | ~5.9k | Automated safety check: Pass | MIT | |
| Paper and Web Source Analyzerjuliye2025/evil-read-arxiv | 1.7k | — | ~715 | Automated safety check: Pass | None | |
| Research Vault Literature Retrievalcheneternity/Research-Vault-Literature-Retrieval | 292 | — | ~2.3k | Automated safety check: Pass | None | |
| Paper Auditbahayonghang/academic-writing-skills | 500 | — | ~5.1k | Automated safety check: Pass | None |
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Related
Works with
Questions about Sophosia Reference Guide
What does Sophosia Reference Guide do?
Reference manager with PDF viewer and Markdown note support. An agent skill from wentorai/research-plugins. Sophosia Reference Guide is an agent skill from wentorai/research-plugins.
When should I use Sophosia Reference Guide?
Sophosia Reference Guide fits situations like: tasks that involve Note-taking; tasks that involve Citation management; tasks that involve PDF.
How do I install Sophosia Reference Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill sophosia-reference-guide -a claude-code`. Or copy the skill folder (skills/literature/metadata/sophosia-reference-guide in wentorai/research-plugins) into .claude/skills/sophosia-reference-guide in your project. Claude Code loads it when a task matches its description.
How do I install Sophosia Reference Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill sophosia-reference-guide -a codex`. Or copy the skill folder (skills/literature/metadata/sophosia-reference-guide in wentorai/research-plugins) into .agents/skills/sophosia-reference-guide in your project. Codex loads it when a task matches its description.
Can I use Sophosia Reference 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 sophosia-reference-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/sophosia-reference-guide, .gemini/skills/sophosia-reference-guide, .github/skills/sophosia-reference-guide and .opencode/skills/sophosia-reference-guide in your project.
What does Sophosia Reference Guide need to run?
Going by SKILL.md and its folder, Sophosia Reference Guide needs the command-line tools its instructions call (npm and git). Our summary lists: Node.js.
Does Sophosia Reference Guide access the network?
SKILL.md names 2 domains. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. As links in the text: excalidraw.com. This is read from the text; nothing was executed.
Is Sophosia Reference 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 Sophosia Reference Guide use?
Sophosia Reference 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 Sophosia Reference Guide use?
About 810 tokens (SKILL.md is roughly 3.2k 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 Sophosia Reference Guide?
Skills that share tags, products or a category with Sophosia Reference Guide: Obsidian Paper Vault (Aperivue/medsci-skills, 333 stars), Ref Downloader (ltczding-gif/ref-downloader, 139 stars), Paper and Web Source Analyzer (juliye2025/evil-read-arxiv, 1.7k stars) and Research Vault Literature Retrieval (cheneternity/Research-Vault-Literature-Retrieval, 292 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Sophosia Reference 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.