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AxoWise User Guide

Overview

AxoWise is designed to help you develop contextual biological insights using protein interaction data, functional relationships, and literature-based knowledge extraction. It leverages multiple interconnected networks and advanced AI-driven techniques to provide meaningful insights.

Networks in AxoWise

AxoWise integrates three key networks:

  • Protein Network: Identifies and clusters protein communities based on interaction data, helping uncover functional modules.
  • Function Network: Maps functional relationships between proteins to explore biological roles and interactions.
  • Publication Network: Extracts relevant abstracts and knowledge from literature, linking biological concepts with scientific publications.

Graph Retrieval Augmented Generation (GRAG)

AxoWise utilizes Graph Retrieval Augmented Generation (GRAG) to enhance biological insight extraction by integrating vector database retrieval with AI-driven summarization. This approach efficiently retrieves structured biological knowledge, enabling more accurate and context-aware exploration of biological networks and literature.

By leveraging:

  • Vector Database Retrieval, AxoWise efficiently indexes and searches high-dimensional biological data, allowing for rapid similarity-based queries across publication networks.
  • Graph Retrieval, which extracts relevant interconnected biological entities, ensuring retrieved data maintains structural and contextual relevance.
  • Augmented Generation, utilizing AI-powered summarization and text generation to synthesize retrieved knowledge into actionable insights, integrating findings from multiple sources into a cohesive narrative.

Installation & Setup

To install and set up AxoWise, follow the Installation & Setup Guide. This section provides step-by-step instructions for installing dependencies, setting up the environment, and running AxoWise.

Quick Start

To get started with AxoWise quickly, follow the Quick Start Guide.

This guide provides a *hands-on example* to help you start using AxoWise immediately. Follow it to input proteins, analyze networks, and extract insights in just a few steps!

Detailed Topics

Ready to dive deeper? Select a section below to learn how to set up, analyze data, and extract meaningful biological insights using AxoWise.

  1. Input Data → Learn about supported input formats, including protein lists and annotated tables.
  2. Protein Network → Detecting and clustering protein communities to uncover functional modules.
  3. Function Network → Understanding biological roles and relationships between proteins.
  4. Publication Network → Extracting relevant literature-based knowledge from curated sources.
  5. AI Extraction → Using AI-driven techniques to summarize and generate insights from retrieved knowledge.
  6. Troubleshooting → Resolving common issues and optimizing AxoWise usage.