---
name: sophosia-reference-guide
description: "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

```bash
# 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

```markdown
### 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

```markdown
### 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
### 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

```markdown
### 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

- [Sophosia GitHub](https://github.com/sophosia/sophosia)
- [Excalidraw](https://excalidraw.com/)


---
Source attribution: wentorai
Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/literature/metadata/sophosia-reference-guide/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Dave AI.

## Upstream license notice

MIT License

Copyright (c) 2026 Wentor AI

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Dave AI resource metadata

Creator / publisher: wentorai
Original project: https://github.com/wentorai/research-plugins/blob/bf44b3cd617fa94c8a1b254c5d1987142ca3d631/skills/literature/metadata/sophosia-reference-guide/SKILL.md
Attribution basis: Source repository record

Fields of work: Content & Media, Education & Research, Marketing, Product Management
Roles: Academic Writer, Content Marketer, Copywriter, Product Manager, Researcher
Specialties: Notion
Tools: Excalidraw, Sophosia
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 0ee8b1c2b90b08a0c158700300b516c6ab644d225599a4b69085f712929606b3