Imported from wentorai/research-plugins (skills/literature/metadata/sophosia-reference-guide/SKILL.md). Install upstream with npx skills add wentorai/research-plugins --skill sophosia-reference-guide. Copyright stays with the author.

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 build

Features

### 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 summaries

Workspace 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 presentations

Import/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 lists

Use 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

Install sophosia-reference-guide and it becomes one more candidate the router can pick - when it fits.

A listing is a routing target with a manifest: what it does, which domains it covers, what it costs and who publishes it. Once installed it sits beside your own models and tools, is scored like any other candidate for each request, and shows up in the trace when it wins. Ratings come from workspaces that installed it, one per account.

sophosia-reference-guide

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