paper-tree 0.1.0

A Python library for building and analyzing academic paper citation trees

Paper Tree

A Python library for building and analyzing academic paper citation trees using the Semantic Scholar API.

Features

• 🌳 Build Citation Trees: Construct citation networks starting from any paper
• 🔍 Automatic Deduplication: Efficiently handle papers cited multiple times
• 📊 Flexible Depth Control: Customize how deep to traverse the citation network
• 💾 Multiple Export Formats: Save to JSON or PostgreSQL
• 🚀 Rate Limit Handling: Built-in retry logic and rate limiting
• 📈 Rich Metadata: Track depth, citations, authors, and references

Installation

Basic Installation

pip install paper-tree

With PostgreSQL Support

pip install paper-tree[postgres]

Development Installation

git clone https://github.com/clodlingxi/paper_tree.git
cd paper_tree
pip install -e .[dev]

Quick Start

Building a Citation Tree

from paper_tree import CitationTreeBuilder

# Initialize builder with API key (optional but recommended)
builder = CitationTreeBuilder(api_key="your_semantic_scholar_api_key")

# Build citation tree starting from a paper
tree = builder.build_tree("ARXIV:1706.03762", max_depth=2)

print(f"Built tree with {len(tree)} papers")
print(f"Root paper: {tree.root_title}")

Exporting to JSON

from paper_tree import JSONExporter

tree = {""} # Your Json

# Export to JSON file
exporter = JSONExporter()
exporter.export(tree, "citation_tree.json")

Exporting to PostgreSQL

from paper_tree import PostgreSQLExporter

tree = {""} # Your Json

# Configure database connection
db_exporter = PostgreSQLExporter(
    host="localhost",
    database="paper_db",
    user="postgres",
    password="your_password",
    table_name="citation_tree"
)

# Export to database
db_exporter.export(tree, drop_existing=True)

Usage Examples

Basic Citation Tree

from paper_tree import CitationTreeBuilder, JSONExporter

# Create builder
builder = CitationTreeBuilder(api_key="your_api_key")

# Build tree from "Attention is All you Need" paper
tree = builder.build_tree("ARXIV:1706.03762", max_depth=2)

# Get statistics
stats = tree.get_statistics()
print(f"Total papers: {stats['total_papers']}")
print(f"Max depth: {stats['max_depth']}")
print(f"Papers by depth: {stats['papers_by_depth']}")

# Export to JSON
JSONExporter.export(tree, "attention_tree.json")

Building Multiple Trees

from paper_tree import CitationTreeBuilder

builder = CitationTreeBuilder(api_key="your_api_key")

# Build trees from multiple root papers
root_papers = [
    "ARXIV:1706.03762",  # Attention is All you Need
    "ARXIV:1512.03385",  # ResNet
    "ARXIV:1409.0473",   # GoogLeNet
]

trees = builder.build_tree_from_multiple_roots(root_papers, max_depth=1)

for tree in trees:
    print(f"{tree.root_title}: {len(tree)} papers")

Working with Papers

tree = {""} # Your Json

# Get root paper
root = tree.get_root_paper()
print(f"Title: {root.title}")
print(f"Year: {root.year}")
print(f"Citations: {root.citation_count}")

# Get papers at specific depth
depth_1_papers = tree.get_papers_by_depth(1)
print(f"Found {len(depth_1_papers)} papers at depth 1")

# Check if paper exists in tree
if "some_paper_id" in tree:
    paper = tree.get_paper("some_paper_id")
    print(f"Found: {paper.title}")

Context Manager Usage

from paper_tree import CitationTreeBuilder

# Use context manager for automatic cleanup
with CitationTreeBuilder(api_key="your_api_key") as builder:
    tree = builder.build_tree("ARXIV:1706.03762", max_depth=2)
    # API session is automatically closed

API Reference

CitationTreeBuilder

Main class for building citation trees.

Parameters:

• api_key (str, optional): Semantic Scholar API key
• rate_limit_delay (float): Delay between API requests in seconds (default: 1.5)
• max_retries (int): Maximum retry attempts for failed requests (default: 3)

Methods:

• build_tree(root_paper_id, max_depth=2, verbose=True): Build a citation tree
• build_tree_from_multiple_roots(root_paper_ids, max_depth=2, verbose=True): Build multiple trees
• close(): Close the API session

CitationTree

Represents a citation tree structure.

Properties:

• root_title: Title of the root paper
• size: Total number of papers
• max_depth: Maximum depth in the tree

Methods:

• get_paper(paper_id): Get a paper by ID
• get_papers_by_depth(depth): Get all papers at a specific depth
• get_root_paper(): Get the root paper
• to_dict(): Convert to dictionary format
• get_statistics(): Get tree statistics

JSONExporter

Export citation trees to JSON format.

Methods:

• export(tree, filename, indent=2, ensure_ascii=False): Export tree to JSON file
• load(filename): Load tree from JSON file (returns dict)

PostgreSQLExporter

Export citation trees to PostgreSQL database.

Parameters:

• host (str): Database host (default: 'localhost')
• port (int): Database port (default: 5432)
• database (str): Database name (default: 'paper_db')
• user (str): Database user (default: 'postgres')
• password (str): Database password
• table_name (str): Table name (default: 'citation_tree')

Methods:

• export(tree, drop_existing=False, verbose=True): Export tree to database

Data Structure

Paper Object

Each paper contains:

• paper_id: Unique identifier
• title: Paper title
• year: Publication year
• citation_count: Number of citations
• abstract: Paper abstract
• authors: List of authors (with id and name)
• depth: Depth in the citation tree (0 = root)
• references: List of referenced paper IDs

Database Schema

When exporting to PostgreSQL, the following table is created:

CREATE TABLE citation_tree (
    paper_id VARCHAR(255) PRIMARY KEY,
    title TEXT,
    year INTEGER,
    citation_count INTEGER,
    abstract TEXT,
    authors JSONB,
    depth INTEGER NOT NULL,
    "references" JSONB,
    root_title TEXT NOT NULL,
    created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
);

Configuration

API Rate Limits

The library automatically handles Semantic Scholar API rate limits:

• Default delay: 1.5 seconds between requests
• Automatic retry with exponential backoff on 429 errors
• Batch requests up to 500 papers per call

Getting an API Key

While optional, using an API key provides higher rate limits:

1. Visit Semantic Scholar API
2. Sign up for an API key
3. Use it when initializing the builder:

from paper_tree import CitationTreeBuilder
builder = CitationTreeBuilder(api_key="your_api_key_here")

Examples

See the examples/ directory for more detailed examples:

• examples/basic_usage.py: Basic citation tree building
• examples/export_json.py: JSON export example
• examples/export_postgres.py: PostgreSQL export example
• examples/analyze_tree.py: Tree analysis and statistics

Requirements

• Python >= 3.8
• requests >= 2.28.0
• psycopg2-binary >= 2.9.0 (for PostgreSQL support)

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this library in your research, please cite:

@software{paper_tree,
  title = {Paper Tree: A Python Library for Citation Tree Analysis},
  author = {Paper Tree Contributors},
  year = {2025},
  url = {https://github.com/clodlingxi/paper_tree}
}

Acknowledgments

• Data provided by Semantic Scholar API
• Inspired by the need for better citation network analysis tools

Support

• 📫 Issues: GitHub Issues
• 📖 Documentation: GitHub Wiki
• 💬 Discussions: GitHub Discussions