ExposoGraph

ExposoGraph is a Python toolkit for building, curating, and exporting carcinogen metabolism knowledge graphs using LLM-powered extraction and manual entry.

Part of the CarcinoGenomic Platform — a 5-layer computational pipeline for individualized carcinogen metabolism risk assessment from germline DNA.

Version: 0.0.4 Developed by: Data analysis team @ KaziLab Contact: exposograph@kazilab.se Copyright: KaziLab

The current release separates two control layers:

• Graph mode for ingestion: exploratory or strict

• Graph visibility for viewing and export: all, validated_only, or exploratory_only

Note

This project is under active development.

Note

Parts of this documentation and code were created with assistance from ChatGPT Codex and Claude Code.

Getting Started

• Quick Start
  • Installation
  • Streamlit App
  • Jupyter
  • Advanced Viewer
  • Python Library
• Deployment
  • Streamlit Cloud
  • Local Development
  • PyPI Publishing

User Guide

• Schema Reference
  • Node Types
  • Edge Types
  • Annotation Fields
  • Structured Provenance
  • Grounding and Match Metadata
  • Curation Fields
  • Validation
• Gene Panels & Activity Scores
  • Tier 1: Core Panel (13 genes)
  • Tier 2: Extended Panel (23 genes)
  • Activity Scores

API Reference

• ExposoGraph.config
  • AppMode
  • GraphMode
  • GraphVisibility
  • normalize_app_mode()
  • normalize_graph_mode()
  • normalize_graph_visibility()
  • get_app_mode()
  • persistence_enabled()
• ExposoGraph.models
  • Enums
  • Models
• ExposoGraph.engine
  • GraphEngine
• ExposoGraph.graph_analysis
  • MetabolismChain
  • VariantImpact
  • shortest_path()
  • all_shortest_paths()
  • centrality()
  • metabolism_chain()
  • pathway_subgraph()
  • variant_impact_score()
  • compute_edge_weights()
• ExposoGraph.exporter
  • parse_graph_data_text()
  • parse_graph_data_js()
  • parse_graph_html()
  • parse_graph_artifact()
  • to_graph_data_js()
  • to_plotly_figure()
  • to_plotly_html_string()
  • to_plotly_html()
  • to_interactive_html_string()
  • bundle_to_html_string()
  • to_interactive_html()
  • ensure_viewer_bundle()
  • export_viewer_bundle()
  • to_json()
  • to_gexf()
• ExposoGraph.cytoscape_adapter
  • ViewerLayoutMode
  • CytoscapeBundle
  • normalize_viewer_layout_mode()
  • compute_viewer_positions()
  • load_viewer_positions()
  • load_cytoscape_bundle()
  • write_viewer_positions()
  • viewer_stylesheet()
  • viewer_layout()
  • build_cytoscape_elements()
  • build_cytoscape_metadata()
  • build_cytoscape_bundle()
  • write_cytoscape_bundle()
• ExposoGraph.viewer_dash
  • ViewerState
  • apply_viewer_filters()
  • build_detail_payload()
  • create_dash_viewer_app()
  • launch_dash_viewer()
• ExposoGraph.graph_filters
  • graph_visibility_label()
  • filter_knowledge_graph()
  • filtered_engine()
• ExposoGraph.grounding
  • GroundingMatch
  • normalize_grounding_key()
  • build_graph_grounding_index()
  • build_iarc_grounding_index()
  • build_default_grounding_index()
  • ground_node()
  • ground_knowledge_graph()
  • prepare_knowledge_graph()
• ExposoGraph.llm_extractor
  • extract_graph()
  • ExposoGraph.llm_extractor.SYSTEM_PROMPT
  • ExposoGraph.llm_extractor.EXAMPLE_INPUT
• ExposoGraph.db_clients
  • KEGG notes
• ExposoGraph.seeder
  • seed_from_kegg_pathway()
  • seed_from_ctd()
  • seed_iarc_classification()
• ExposoGraph.example_graphs
  • Data Structures
  • Showcase Builders
• ExposoGraph.reference_data
  • Gene Panel Data
  • Panel Builders
  • Lookups
• ExposoGraph.storage
  • GraphRevisionSummary
  • GraphRevision
  • GraphRepository

Project

• Changelog