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sophosia-reference-guide

Reference manager with PDF viewer and Markdown note support

Published by brycewang-stanford ↗brycewang-stanford/Auto-Empirical-Research-Skills

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sophosia-reference-guide

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Use sophosia-reference-guide to organize [paper collection] into tags and collections, and create Markdown outline notes linked to PDF annotations with BibTeX bibliography support.

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  • [paper collection]

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SKILL.md

name: sophosia-reference-guidedescription: "Reference manager with PDF viewer and Markdown note support"metadata:   openclaw:     emoji: "📚"    category: "literature"    subcategory: "metadata"    keywords: ["reference manager", "PDF viewer", "Markdown notes", "Excalidraw", "paper organization", "open source"]    source: "https://github.com/sophosia/sophosia"

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

  1. Reading workflow: PDF + notes in single workspace
  2. Visual thinking: Excalidraw diagrams alongside papers
  3. Literature review: Linked notes across paper collection
  4. Presentation prep: Visual notes exportable as diagrams
  5. Research journal: Rich per-paper documentation

References