ScholarGraph

Academic literature intelligence toolkit for multi-source paper search, analysis, and knowledge graph building with AI assistance.

Josephyb97@josephyb97

Install

openclaw skills install @josephyb97/scholargraph

ScholarGraph - Academic Literature Intelligence Toolkit

Overview

ScholarGraph is a comprehensive academic literature intelligence toolkit that helps researchers efficiently search, analyze, and manage academic papers using AI-powered tools. Features 11 academic search sources with intelligent domain-based source selection and PDF download capabilities.

Security & Privacy

This skill operates with the following permissions:

Network Access: Queries academic APIs (arXiv, Semantic Scholar, OpenAlex, PubMed, CrossRef, DBLP, IEEE, CORE, Google Scholar, Unpaywall) and web search services
File System: Reads/writes configuration files, downloads PDFs, stores knowledge graphs in SQLite database (data/knowledge-graphs.db)
LLM Integration: Sends custom system prompts to AI providers for structured JSON output (concept extraction, paper analysis, etc.)
Optional Python: PDF figure extraction (pymupdf) and PPT export (python-pptx) require Python 3.8+

Data Storage: All data is stored locally. No telemetry or analytics are collected.

API Keys: Optional API keys are only used for their respective services and are never transmitted elsewhere.

Source Code: Open source under MIT license at https://github.com/Josephyb97/ScholarGraph

Features

Core Modules (6)

Literature Search - Multi-source academic paper discovery (11 sources)
- Free sources: arXiv, Semantic Scholar, OpenAlex (250M+), PubMed (biomedical), CrossRef (150M+ DOI), DBLP (CS), Web Search
- API-key sources: IEEE Xplore, CORE, Google Scholar (SerpAPI), Unpaywall (OA PDF)
- Adapter-based plugin architecture for easy extension
- Complementary search strategy with auto domain detection (biomedical/cs/engineering/physics)
- Priority-based source selection per domain
- Query expansion for better search results
- PDF download with multi-strategy URL resolution
Concept Learner - Rapid knowledge framework construction
- Generate structured learning cards
- Include code examples and related papers
- Support beginner/intermediate/advanced depth levels
Knowledge Gap Detector - Proactive blind spot identification
- Analyze knowledge coverage in specific domains
- Identify critical, recommended, and optional gaps
- Provide learning recommendations and time estimates
Progress Tracker - Real-time field monitoring
- Track research topics and keywords
- Generate daily/weekly/monthly reports
- Monitor trending papers and topics
Paper Analyzer - Deep paper analysis
- Extract key contributions and insights
- Support quick/standard/deep analysis modes
- Generate structured analysis reports
Knowledge Graph Builder - Concept relationship visualization
- Build interactive knowledge graphs
- Support Mermaid and JSON output formats
- Find learning paths between concepts
- SQLite-based persistent storage
- Bidirectional concept-paper indexing

Advanced Features (9)

Review Detector - Automatic review paper identification
- Multi-dimensional scoring (title 30% + citations 25% + abstract 25% + AI 20%)
- Chinese and English keyword support
- Confidence-based filtering with user confirmation
Concept Extractor - Extract concepts from review papers
- AI-powered extraction of 15-30 core concepts
- Four-level categorization (foundation/core/advanced/application)
- Importance scoring and relationship identification
- Cross-review deduplication and merging
Review-to-Graph Workflow - End-to-end pipeline
- Search reviews -> Detect -> Confirm -> Analyze -> Extract concepts
- Build knowledge graph -> Enrich with key papers -> Index -> Store
- Interactive or automatic confirmation mode
Knowledge Graph Query - Bidirectional literature indexing
- Concept -> papers: find papers related to a concept
- Paper -> concepts: find concepts covered by a paper
- Paper recommendations based on multiple concepts
- SQLite-optimized high-performance queries
Compare Concepts - Compare two concepts
- Identify similarities and differences
- Provide use case recommendations
Compare Papers - Compare multiple papers
- Find common themes and differences
- Generate synthesis analysis
Critique - Critical paper analysis
- Identify strengths and weaknesses
- Find research gaps and improvement suggestions
- Support custom focus areas
Learning Path - Find optimal learning paths
- Discover paths between concepts
- Generate topological learning order
- Visualize with Mermaid diagrams
Graph Management - Manage persistent knowledge graphs
- List all saved graphs
- View graph statistics
- Export graphs to JSON
- Visualize with Mermaid
Paper Visualization - Interactive paper presentation
- Convert paper analysis to HTML slide presentations
- Academic dark/light themes with responsive typography
- Keyboard/touch/scroll navigation, edit mode (E key)
- PDF figure extraction (pymupdf) and PPT export (python-pptx)
- 8+ slides: title, abstract, key points, methodology, experiments, contributions, limitations, references
Interactive Knowledge Graph - D3.js force-directed visualization
- Convert knowledge graphs to interactive HTML with D3.js v7
- Node size reflects paper count, edge thickness reflects concept tightness
- Zoom/pan, node dragging, click-to-detail panel, search, legend
- Paper preview bridge: click "View Presentation" to open paper slides in new tab
- Category colors: foundation=#4FC3F7, core=#FFB74D, advanced=#CE93D8, application=#81C784

Technical Features

11 Academic Search Sources: arXiv, Semantic Scholar, OpenAlex, PubMed, CrossRef, DBLP, IEEE Xplore, CORE, Google Scholar, Unpaywall, Web Search
Complementary Search Strategy: Auto-detects query domain and selects optimal source combination
Adapter Pattern: Plugin-based search source architecture for easy extension
PDF Download: Multi-strategy URL resolution (direct, Unpaywall, OpenAlex OA, CORE)
Multi-AI Provider Support: 15+ AI providers including OpenAI, Anthropic, DeepSeek, Qwen, Zhipu AI, etc.
SQLite Persistence: Knowledge graphs stored in SQLite database via bun:sqlite
Bidirectional Indexing: Concept-paper and paper-concept bidirectional query support
Rate Limiting: Per-source rate limiting with automatic retry and delay
Interactive HTML Output: Paper slide presentations, D3.js knowledge graph visualizations
Multiple Output Formats: Markdown, JSON, Mermaid, HTML, PPTX
TypeScript + Bun: Fast and type-safe runtime
CLI + API: Both command-line and programmatic interfaces

Installation

bash

# Clone repository
git clone https://github.com/Josephyb97/ScholarGraph.git
cd ScholarGraph

# Install dependencies
bun install

# Initialize configuration
bun run cli.ts config init

Configuration

Set up your AI provider:

bash

# Using OpenAI
export AI_PROVIDER=openai
export OPENAI_API_KEY="your-api-key"

# Using DeepSeek
export AI_PROVIDER=deepseek
export DEEPSEEK_API_KEY="your-api-key"

# Using Qwen (通义千问)
export AI_PROVIDER=qwen
export QWEN_API_KEY="your-api-key"

Academic Source API Keys (optional, expand search coverage)

bash

export NCBI_API_KEY="your-key"           # PubMed high-speed access (10 req/s)
export IEEE_API_KEY="your-key"           # IEEE Xplore engineering papers
export CORE_API_KEY="your-key"           # CORE open access full text
export UNPAYWALL_EMAIL="your@email.com"  # Unpaywall OA PDF resolver
export CROSSREF_MAILTO="your@email.com"  # CrossRef polite pool (higher rate)
export SERPAPI_KEY="your-key"            # Google Scholar (via SerpAPI)
export SERPER_API_KEY="your-key"         # Web search via Serper

Usage Examples

Search Literature

bash

# Auto-select best sources based on query domain
lit search "transformer attention" --limit 20

# Specify domain for optimized source selection
lit search "CRISPR gene editing" --domain biomedical

# Use specific sources (comma-separated)
lit search "deep learning" --source semantic_scholar,arxiv,openalex --sort citations

# Search and download PDFs
lit search "attention is all you need" --download --limit 3

Download PDFs

bash

# Search and download PDFs
lit download "transformer" --limit 5 --output ./papers

Learn Concepts

bash

lit learn "BERT" --depth advanced --papers --code --output bert-card.md

Detect Knowledge Gaps

bash

lit detect --domain "Deep Learning" --known "CNN,RNN" --output gaps.md

Analyze Papers

bash

lit analyze "https://arxiv.org/abs/1706.03762" --mode deep --output analysis.md

Build Knowledge Graph

bash

lit graph transformer attention BERT GPT --format mermaid --output graph.md

Compare Concepts

bash

lit compare concepts CNN RNN --output comparison.md

Compare Papers

bash

lit compare papers "url1" "url2" "url3" --output comparison.md

Critical Analysis

bash

lit critique "paper-url" --focus "novelty,scalability" --output critique.md

Find Learning Path

bash

lit path "Machine Learning" "Deep Learning" --concepts "Neural Networks" --output path.md

Search Review Papers

bash

lit review-search "attention mechanism" --limit 10

Build Knowledge Graph from Reviews

bash

# From search query (interactive mode)
lit review-graph "deep learning" --output dl-graph --enrich

# From specific URL
lit review-graph "https://arxiv.org/abs/xxxx" --output my-graph --enrich

# Auto-confirm mode (non-interactive)
lit review-graph "transformer" --output tf-graph --enrich --auto-confirm

Query Knowledge Graph

bash

# Find papers by concept
lit query concept "transformer" --graph dl-graph --limit 20

# Find concepts by paper
lit query paper "https://arxiv.org/abs/1706.03762" --graph dl-graph

Manage Knowledge Graphs

bash

# List all graphs
lit graph-list

# View graph statistics
lit graph-stats dl-graph

# Visualize graph
lit graph-viz dl-graph --format mermaid --output graph.md

# Export graph
lit graph-export dl-graph --output dl-graph.json

Paper Visualization

bash

# Generate interactive HTML presentation
lit paper-viz "https://arxiv.org/abs/1706.03762" --output attention.html

# With theme and PPT export
lit paper-viz "https://arxiv.org/abs/1706.03762" --mode deep --theme academic-light --ppt

# Manually provide figures
lit paper-viz "https://example.com/paper" --figures ./my-figures

Interactive Knowledge Graph

bash

# Generate interactive D3.js graph from existing knowledge graph
lit graph-interactive dl-graph --output dl-interactive.html

# Without paper data (lighter weight)
lit graph-interactive my-graph --no-paper-viz

Use Cases

1. Quick Field Onboarding

Learn core concepts
Detect prerequisite gaps
Build knowledge graph
Plan learning path

2. Deep Paper Understanding

Analyze paper in depth
Perform critical analysis
Learn new concepts from paper
Compare with related papers

3. Research Progress Tracking

Monitor research topics
Track latest papers
Generate progress reports

4. Concept Comparison

Compare technical approaches
Evaluate different models
Build comparison graphs

5. Review-Driven Knowledge Building

Search and identify review papers
Extract concepts from reviews
Build persistent knowledge graphs
Query concept-paper relationships

6. Paper Visualization & Graph Exploration

Analyze paper and generate interactive HTML presentation
Build knowledge graph from reviews
Generate interactive D3.js graph with paper preview
Click nodes to view paper details and open presentations

Project Structure

text

ScholarGraph/
├── cli.ts                      # Unified CLI entry
├── config.ts                   # Configuration management
├── README.md                   # Project documentation
├── CHANGELOG.md                # Version history
├── SKILL.md                    # This file
│
├── shared/                     # Shared modules
│   ├── ai-provider.ts          # AI provider abstraction
│   ├── types.ts                # Type definitions
│   ├── validators.ts           # Parameter validation
│   ├── errors.ts               # Error handling
│   └── utils.ts                # Utility functions
│
├── literature-search/          # Literature search module
│   └── scripts/
│       ├── search.ts           # Search engine core
│       ├── types.ts            # Type definitions
│       ├── query-expander.ts   # Query expansion
│       ├── search-strategy.ts  # Complementary search strategy
│       ├── pdf-downloader.ts   # PDF download module
│       └── adapters/           # Search source adapters
│           ├── base.ts         # Adapter interface & base class
│           ├── registry.ts     # Adapter registry
│           ├── index.ts        # Barrel export
│           ├── arxiv-adapter.ts
│           ├── semantic-scholar-adapter.ts
│           ├── web-adapter.ts
│           ├── openalex-adapter.ts
│           ├── pubmed-adapter.ts
│           ├── crossref-adapter.ts
│           ├── dblp-adapter.ts
│           ├── ieee-adapter.ts
│           ├── core-adapter.ts
│           ├── unpaywall-adapter.ts
│           └── google-scholar-adapter.ts
│
├── concept-learner/            # Concept learning module
├── knowledge-gap-detector/     # Gap detection module
├── progress-tracker/           # Progress tracking module
├── paper-analyzer/             # Paper analysis module
│
├── review-detector/            # Review paper identification
│   └── scripts/
│       ├── detect.ts           # Multi-dimensional scoring
│       └── types.ts
│
├── concept-extractor/          # Concept extraction from reviews
│   └── scripts/
│       ├── extract.ts          # AI-powered extraction
│       └── types.ts
│
├── knowledge-graph/            # Knowledge graph module
│   └── scripts/
│       ├── graph.ts            # Graph building core
│       ├── indexer.ts          # Bidirectional indexing
│       ├── storage.ts          # SQLite persistence
│       └── enricher.ts         # Key paper association
│
├── paper-viz/                  # Paper visualization
│   └── scripts/
│       ├── types.ts            # Presentation data interfaces
│       ├── slide-builder.ts    # PaperAnalysis → slides
│       ├── html-generator.ts   # Self-contained HTML generation
│       ├── pdf-figure-extractor.ts  # PDF figure extraction (pymupdf)
│       └── ppt-exporter.ts     # PPT export (python-pptx)
│
├── graph-viz/                  # Interactive knowledge graph
│   └── scripts/
│       ├── types.ts            # D3 graph data interfaces
│       ├── graph-data-adapter.ts # KnowledgeGraph → D3 data
│       ├── html-generator.ts   # Interactive HTML (D3.js v7)
│       └── paper-viz-bridge.ts # Graph → paper presentation bridge
│
├── workflows/                  # End-to-end workflows
│   └── review-to-graph.ts      # Review to graph pipeline
│
├── data/                       # Data directory (auto-created)
│   └── knowledge-graphs.db     # SQLite database
│
├── downloads/                  # PDF downloads (auto-created)
│   └── pdfs/
│       └── metadata.json       # Download index
│
└── test/                       # Tests and documentation
    ├── ADVANCED_FEATURES.md
    ├── TEST_RESULTS.md
    └── scripts/

Supported AI Providers

International

OpenAI
Anthropic (Claude)
Azure OpenAI
Groq
Together AI
Ollama (local)

China

通义千问 (Qwen/DashScope)
DeepSeek
智谱 AI (GLM)
MiniMax
Moonshot (Kimi)
百川 AI (Baichuan)
零一万物 (Yi)
豆包 (Doubao)

Output Formats

Markdown Reports

Concept cards with definitions, components, history, applications
Gap reports with analysis and recommendations
Progress reports with trending topics
Paper analyses with methods, experiments, contributions
Comparison analyses with similarities and differences
Critical analyses with strengths, weaknesses, and suggestions

JSON Data

Structured data for programmatic processing

Mermaid Diagrams

Interactive knowledge graphs and learning paths

Interactive HTML

Paper slide presentations with keyboard/scroll/touch navigation
D3.js force-directed knowledge graph with zoom, search, and paper panel

Requirements

Bun 1.3+ or Node.js 18+
AI provider API key
Internet connection for paper search
Python 3.8+ (optional, for PDF figure extraction and PPT export)

License

MIT License

Version

Current version: 1.0.0

Author

ScholarGraph Team

Design Inspirations:

frontend-slides - Paper slide presentation design reference
Argo Scholar - Interactive knowledge graph design reference

For detailed documentation, see README.md For advanced features, see test/ADVANCED_FEATURES.md For test results, see test/TEST_RESULTS.md

ScholarGraph

Install

ScholarGraph - Academic Literature Intelligence Toolkit

Overview

Security & Privacy

Features

Core Modules (6)

Advanced Features (9)

Technical Features

Installation

Configuration

Academic Source API Keys (optional, expand search coverage)

Usage Examples

Search Literature

Download PDFs

Learn Concepts

Detect Knowledge Gaps

Analyze Papers

Build Knowledge Graph

Compare Concepts

Compare Papers

Critical Analysis

Find Learning Path

Search Review Papers

Build Knowledge Graph from Reviews

Query Knowledge Graph

Manage Knowledge Graphs

Paper Visualization

Interactive Knowledge Graph

Use Cases

1. Quick Field Onboarding

2. Deep Paper Understanding

3. Research Progress Tracking

4. Concept Comparison

5. Review-Driven Knowledge Building

6. Paper Visualization & Graph Exploration

Project Structure

Supported AI Providers

International

China

Output Formats

Markdown Reports

JSON Data

Mermaid Diagrams

Interactive HTML

Requirements

License

Links

Version

Author

Related skills