ExposoGraph 0.0.3

ExposoGraph — LLM-powered extraction and manual curation of carcinogen metabolism pathways

ExposoGraph

Build, curate, and export 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: 0.0.3 Developed by: Data analysis team @ KaziLab Contact: [e-mail] Copyright: KaziLab

Acknowledgement

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

Features

• Multi-LLM Extraction — Describe a carcinogen metabolism pathway in plain English; OpenAI (GPT-4o) or local Ollama models extract structured nodes and edges automatically
• Mode-Aware Ingestion — Use exploratory mode to keep provisional entities or strict mode to keep only canonically grounded content
• Manual Entry — Add and annotate nodes and edges with full provenance and curation tracking
• Graph Analysis — Shortest path, centrality, metabolism chain traversal, pathway subgraph, variant impact scoring
• Public DB Integration — KEGG pathway lookups, CTD chemical-gene interactions, IARC carcinogen classifications
• Interactive Preview — Color-coded Streamlit AGraph visualization with hover metadata, search/filter controls, zoom, and downloadable Plotly HTML exports
• Advanced Graph Viewer — Dash Cytoscape viewer with sidebar search, legends, carcinogen filters, detail panel, image export, and saved layout JSON
• Validated vs Exploratory Views — Filter the current graph to all, validated only, or exploratory only in the UI and export pipeline
• Rich Annotations — Structured provenance records, source manifests, curated KEGG pathway coverage, PubMed IDs, tissue context, pharmacogenomic variants, activity scores
• Multiple Export Formats — Standalone Plotly HTML, parseable app HTML, JSON, D3.js viewer (graph-data.js), GEXF (Gephi)
• Viewer Data Contract — Export a Cytoscape-ready JSON bundle and saved preset layout for richer web-style exploration without maintaining custom JavaScript
• Validation — Referential integrity checks at model level, dangling edge detection, carcinogen context validation
• Persistent Storage — SQLite-backed revision history with explicit export visibility tracking and atomic operations

Quick Start

Try Without an API Key

A pre-built Benzo[a]pyrene metabolism graph is included:

pip install -e .
python examples/build_bap_graph.py

This loads examples/bap_graph.json (20 nodes, 20 edges covering the full BaP → BPDE → DNA adduct pathway), runs graph analysis, and exports to HTML and JSON.

For a no-API-key demonstration of strict vs exploratory handling and validated-only exports:

python examples/mode_visibility_demo.py

Sample output

Loaded graph: 20 nodes, 20 edges

Shortest path CYP1A1 → BPDE-dG: CYP1A1 → BPDE → BPDE_dG

Top-5 nodes by degree centrality:
  CYP1A1        0.263
  BPDE          0.211
  CYP1B1        0.158
  BPDE_dG       0.158
  BPDE_GSH      0.158

BaP metabolism chain: 16 nodes, 13 edges
  Activation edges:    4
  Detoxification edges: 3
  Adduct edges:        1
  Repair edges:        3

Variant impact score for CYP1A1:
  Activity score:        1.0
  Downstream adducts:    1
  Impact score:          1.00

Sample JSON

{
  "nodes": [
    {"id": "BaP", "label": "Benzo[a]pyrene", "type": "Carcinogen", "group": "PAH", "iarc": "Group 1"},
    {"id": "CYP1A1", "label": "CYP1A1", "type": "Enzyme", "phase": "I", "role": "Activation"},
    {"id": "BPDE", "label": "BPDE", "type": "Metabolite", "reactivity": "High"},
    {"id": "BPDE_dG", "label": "BPDE-N2-dG", "type": "DNA_Adduct"}
  ],
  "edges": [
    {"source": "CYP1A1", "target": "BPDE", "type": "ACTIVATES", "carcinogen": "BaP"},
    {"source": "BPDE", "target": "BPDE_dG", "type": "FORMS_ADDUCT", "carcinogen": "BaP"}
  ]
}

Streamlit App

pip install -e ".[streamlit]"
streamlit run ExposoGraph/app.py

App mode defaults to stateless, which disables server-side saves and is appropriate for public web deployment. To enable local revision history and file saves on your own machine:

export ExposoGraph_MODE=local
streamlit run ExposoGraph/app.py

Jupyter

pip install -e ".[notebook]"
jupyter lab

No notebook file is currently bundled in this repository. Use the installed package from your own notebook, or start from the runnable examples in examples/.

Advanced Viewer

pip install -e ".[viewer]"

from ExposoGraph import (
    GraphVisibility,
    ViewerLayoutMode,
    launch_dash_viewer,
    write_cytoscape_bundle,
)

write_cytoscape_bundle(
    engine,
    "exports/graph_cytoscape.json",
    visibility=GraphVisibility.ALL,
    layout_mode=ViewerLayoutMode.COSE,
)

launch_dash_viewer(
    engine,
    visibility=GraphVisibility.ALL,
    layout_mode=ViewerLayoutMode.COSE,
    port=8050,
)

Python Library

pip install -e .

from ExposoGraph import (
    GraphEngine,
    GraphMode,
    GraphVisibility,
    centrality,
    extract_graph,
    metabolism_chain,
    to_json,
)

# LLM extraction (requires OpenAI API key)
# exploratory: keep unmatched or custom content
kg = extract_graph(
    "Benzo[a]pyrene is activated by CYP1A1...",
    mode=GraphMode.EXPLORATORY,
)
engine = GraphEngine()
engine.merge(kg, mode=GraphMode.EXPLORATORY)

# Analysis
scores = centrality(engine, method="degree")
chain = metabolism_chain(engine, "BaP")

# Visibility-aware export
to_json(engine, "graph_validated.json", visibility=GraphVisibility.VALIDATED_ONLY)

Using Ollama (Local LLM)

from ExposoGraph import GraphMode, extract_graph
from ExposoGraph.llm_backend import OllamaBackend

backend = OllamaBackend(base_url="http://localhost:11434")
kg = extract_graph(
    "BaP is activated by CYP1A1...",
    backend=backend,
    model="llama3.1",
    mode=GraphMode.EXPLORATORY,
)

Public Database Integration

from ExposoGraph import GraphMode
from ExposoGraph.db_clients import IARCClassifier
from ExposoGraph.seeder import seed_from_ctd, seed_from_kegg_pathway

# Seed from KEGG pathway
kg = seed_from_kegg_pathway("hsa05204", mode=GraphMode.STRICT)

# Seed from CTD
kg = seed_from_ctd("Benzo(a)pyrene", mode=GraphMode.EXPLORATORY)

# IARC classification lookup
clf = IARCClassifier()
clf.classify("Benzo[a]pyrene")  # → IARCGroup.GROUP_1

Reference Curation Metadata

from ExposoGraph import CURATION_SOURCE_MANIFEST, REFERENCE_KEGG_PATHWAYS

primary_sources = CURATION_SOURCE_MANIFEST["primary_sources"]
kegg_ids = [entry["pathway_id"] for entry in REFERENCE_KEGG_PATHWAYS]

Manuscript-Aligned Showcase Summary

from ExposoGraph import build_full_legends_architecture_summary

summary = build_full_legends_architecture_summary()

summary.node_count          # 96
summary.edge_count          # 102
summary.node_type_counts    # {'Carcinogen': 15, 'Enzyme': 36, ...}
summary.edge_type_counts    # {'ACTIVATES': 30, 'DETOXIFIES': 23, ...}
summary.carcinogen_classes  # grouped class inventories for section 2.2 rewrites

Optional Androgen Module

from ExposoGraph import build_androgen_module_graph, build_full_legends_graph

androgen_only = build_androgen_module_graph()
showcase_with_androgen = build_full_legends_graph(include_androgen_module=True)

Configuration

Set your OpenAI API key as an environment variable:

export OPENAI_API_KEY="sk-..."

Or enter it in the Streamlit sidebar when running the app.

For Streamlit Cloud deployment, add the key to .streamlit/secrets.toml:

OPENAI_API_KEY = "sk-..."

Graph Modes and Visibility

Two separate controls now shape how data moves through the system:

• Graph mode controls ingestion behavior:
  • exploratory keeps unmatched or custom entities and marks them as provisional
  • strict keeps only canonically grounded nodes and edges
• Graph visibility controls viewing and export behavior:
  • all
  • validated_only
  • exploratory_only

Typical pattern:

from ExposoGraph import (
    GraphEngine,
    GraphMode,
    GraphRepository,
    GraphVisibility,
    ViewerLayoutMode,
    launch_dash_viewer,
    write_cytoscape_bundle,
    extract_graph,
    to_interactive_html,
    to_plotly_html,
)

engine = GraphEngine()
kg = extract_graph(
    "BaP induces CYP1A1 and forms BPDE adducts",
    mode=GraphMode.STRICT,
)
engine.merge(kg, mode=GraphMode.STRICT)

to_interactive_html(
    engine,
    "validated_graph.html",
    visibility=GraphVisibility.VALIDATED_ONLY,
)

to_plotly_html(
    engine,
    "validated_graph_plotly.html",
    visibility=GraphVisibility.VALIDATED_ONLY,
)

write_cytoscape_bundle(
    engine,
    "validated_graph_cytoscape.json",
    visibility=GraphVisibility.VALIDATED_ONLY,
    layout_mode=ViewerLayoutMode.PRESET,
)

with GraphRepository("data/ExposoGraph.sqlite3") as repo:
    repo.save_engine(
        graph_key="bap_validated",
        graph_name="BaP Validated",
        engine=engine,
        visibility=GraphVisibility.VALIDATED_ONLY,
    )

Project Structure

ExposoGraph/
├── __init__.py          # Public API exports
├── app.py               # Streamlit UI orchestrator
├── branding.py          # Version and metadata
├── config.py            # App modes, graph modes, and visibility enums
├── engine.py            # NetworkX-backed graph engine
├── exporter.py          # JSON, D3.js, HTML, GEXF export
├── graph_filters.py     # Validated/exploratory graph filtering helpers
├── graph_analysis.py    # Shortest path, centrality, metabolism chains
├── grounding.py         # Canonical grounding and strict-mode preparation
├── llm_backend.py       # Pluggable LLM backends (OpenAI, Ollama)
├── llm_extractor.py     # LLM prompt + extraction pipeline
├── models.py            # Pydantic data models (Node, Edge, KnowledgeGraph)
├── reference_data.py    # Gene panels and activity scores
├── seeder.py            # DB-to-KnowledgeGraph conversion
├── storage.py           # SQLite revision history
├── db_clients/
│   ├── kegg.py          # KEGG REST API client
│   ├── ctd.py           # CTD chemical-gene interaction client
│   └── iarc.py          # Bundled IARC classification data
├── ui_extract.py        # Tab: LLM extraction
├── ui_manual.py         # Tab: manual node/edge entry
├── ui_preview.py        # Tab: interactive graph preview
└── ui_data.py           # Tab: raw data view
examples/
├── bap_graph.json       # Pre-built BaP metabolism graph (no API key needed)
├── build_bap_graph.py   # Demo script: load → analyze → export
└── mode_visibility_demo.py  # Demo script: strict ingestion + filtered export/save
tests/
├── test_integration.py  # End-to-end pipeline test
├── test_engine.py
├── test_models.py
├── test_exporter.py
├── test_graph_analysis.py
├── test_llm_backend.py
├── test_llm_extractor.py
├── test_db_clients.py
├── test_seeder.py
├── test_reference_data.py
├── test_config.py
└── test_storage.py

Node & Edge Types

Nodes: Carcinogen, Enzyme, Gene, Metabolite, DNA_Adduct, Pathway, Tissue

Edges: ACTIVATES, DETOXIFIES, TRANSPORTS, FORMS_ADDUCT, REPAIRS, PATHWAY, EXPRESSED_IN, INDUCES, INHIBITS, ENCODES, CUSTOM

Development

pip install -e ".[all]"
pytest                           # runs with --cov, 85% threshold gate
ruff check .
mypy ExposoGraph/

Optional dependency groups

Group	Install	Provides
llm	pip install -e ".[llm]"	OpenAI API support
ollama	pip install -e ".[ollama]"	Ollama local LLM support
db	pip install -e ".[db]"	KEGG/CTD HTTP clients
streamlit	pip install -e ".[streamlit]"	Streamlit web app
notebook	pip install -e ".[notebook]"	Jupyter + Plotly/Matplotlib
dev	pip install -e ".[dev]"	pytest, ruff, mypy
docs	pip install -e ".[docs]"	Sphinx + Furo
all	pip install -e ".[all]"	Everything

License

MIT