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sqlite-literature-management-fastmcp-mcp-server

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Created 12/25/2024byYUZongmin

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agentfastmcpllmmcpmemorysqlite

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Python

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Universal Source Management System

A flexible system for managing various types of sources (papers, books, webpages, etc.) and integrating them with knowledge graphs.

Features

Core Features

  • Universal source identification with internal UUID system
  • Support for multiple source types (papers, webpages, books, videos, blogs)
  • Multiple identifier support per source (arxiv, DOI, semantic scholar, ISBN, URL)
  • Structured note-taking with titles and content
  • Status tracking (unread, reading, completed, archived)

Entity Integration

  • Link sources to knowledge graph entities
  • Track relationships between sources and entities
  • Flexible relation types (discusses, introduces, extends, etc.)
  • Integration with memory graph

Prerequisites

This system integrates with the MCP Memory Server for persistent knowledge graph storage.

Quick Start

  1. Create a new SQLite database with our schema:
# Create a new database
sqlite3 sources.db 
        
            
                    relation_type TEXT CHECK(relation_type IN ('discusses', 'introduces', 'extends', 'evaluates', 'applies', 'critiques')),
    notes TEXT,
    PRIMARY KEY (source_id, entity_name)
);

Usage Examples

1. Managing Sources

Add a paper with multiple identifiers:

add_source(
    title="Attention Is All You Need",
    type="paper",
    identifier_type="arxiv",
    identifier_value="1706.03762",
    initial_note={
        "title": "Initial thoughts",
        "content": "Groundbreaking paper introducing transformers..."
    }
)

# Add another identifier to the same paper
add_identifier(
    title="Attention Is All You Need",
    type="paper",
    current_identifier_type="arxiv",
    current_identifier_value="1706.03762",
    new_identifier_type="semantic_scholar",
    new_identifier_value="204e3073870fae3d05bcbc2f6a8e263d9b72e776"
)

Add a webpage:

add_source(
    title="Understanding Transformers",
    type="webpage",
    identifier_type="url",
    identifier_value="https://example.com/transformers",
)

2. Note Taking

Add notes to a source:

add_note(
    title="Attention Is All You Need",
    type="paper",
    identifier_type="arxiv",
    identifier_value="1706.03762",
    note_title="Implementation details",
    note_content="The paper describes the architecture..."
)

3. Entity Linking

Link source to entities:

link_to_entity(
    title="Attention Is All You Need",
    type="paper",
    identifier_type="arxiv",
    identifier_value="1706.03762",
    entity_name="transformer",
    relation_type="introduces",
    notes="First paper to introduce the transformer architecture"
)

Query sources by entity:

get_entity_sources(
    entity_name="transformer",
    type_filter="paper",
    relation_filter="discusses"
)

Best Practices

  1. Source Management

    • Use consistent titles across references

    • Provide as many identifiers as available

                - Keep notes structured with clear titles
      
    • Use appropriate source types

  2. Entity Linking

    • Be specific with relation types
    • Add contextual notes to relationships
    • Verify entity names against memory graph
    • Keep entity relationships focused

Technical Details

  1. Source Identification

    • Internal UUID system for consistent referencing
    • Multiple external identifiers per source
    • Flexible identifier types (arxiv, doi, url, etc.)
    • Title and type based fuzzy matching
  2. Data Organization

    • Structured notes with titles
    • Clear source type categorization
    • Entity relationship tracking
    • Status management

Contributing

  1. Fork the repository
  2. Create a feature branch
  3. Add tests for new features
  4. Submit a pull request
Last updated: 2/7/2025

Publisher info

YUZongmin's avatar

Zongmin Yu

CS & Math Undergraduate Student @ National University of Singapore

Singapore
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followers
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