Drug Interactions & Pharmacogenomics Knowledge Graph

A knowledge graph integrating drug-target interactions, side effects, bioactivity data, and adverse events from 6 open data sources, built on Samyama Graph.

Data Sources

Source	Content	Nodes	License
DrugBank CC0	Drug vocabulary	~12K	CC0
DGIdb	Drug-gene interactions	~20K genes	Open
SIDER	Side effects & indications	~9.4K	CC-BY-SA-4.0
ChEMBL	Bioactivity (IC50, Ki)	~500K	CC-BY-SA-3.0
TTD	Therapeutic targets	~3.4K	CC-BY-NC
OpenFDA FAERS	Adverse events	~15K	Public domain

Quick Start

# 1. Download data
source ~/projects/venv/bin/activate
python -m etl.download_data --data-dir data

# 2. Run tests
pytest tests/ -v

# 3. Load into Samyama
python -m etl.loader --data-dir data --url http://localhost:8080

# 4. Start MCP server
python -m mcp_server.server --url http://localhost:8080

Schema

Drug ──INTERACTS_WITH_GENE──> Gene
Drug ──HAS_SIDE_EFFECT──────> SideEffect
Drug ──HAS_INDICATION───────> Indication
Drug ──HAS_BIOACTIVITY──────> Bioactivity ──BIOACTIVITY_TARGET──> Gene
Drug ──TTD_TARGETS──────────> Target
Drug ──HAS_ADVERSE_EVENT────> AdverseEvent
Drug ──CLASSIFIED_AS────────> DrugClass ──PARENT_CLASS──> DrugClass

Cross-KG Federation

This KG bridges to Pathways KG and Clinical Trials KG:

-- Drug targets → Biological Pathways
MATCH (d:Drug {name: 'Metformin'})-[:INTERACTS_WITH_GENE]->(g:Gene)
MATCH (p:Protein {name: g.gene_name})-[:PARTICIPATES_IN]->(pw:Pathway)
RETURN pw.name, g.gene_name

-- Side effects of drugs in Phase 3 trials
MATCH (d:Drug)-[:HAS_SIDE_EFFECT]->(se:SideEffect)
MATCH (i:Intervention {name: d.name})<-[:TESTS]-(ct:ClinicalTrial)
WHERE ct.phase CONTAINS '3'
RETURN d.name, se.name, ct.nct_id

-- Polypharmacy: shared targets between drugs
MATCH (d1:Drug {name: 'Warfarin'})-[:INTERACTS_WITH_GENE]->(g:Gene)
      <-[:INTERACTS_WITH_GENE]-(d2:Drug {name: 'Aspirin'})
RETURN g.gene_name AS shared_target

MCP Tools

12 domain-specific tools: drug_interactions, gene_drugs, drug_side_effects, drug_indications, drug_bioactivity, drug_adverse_events, interaction_checker, polypharmacy_risk, drug_class_hierarchy, gene_drug_landscape, side_effect_drugs, target_development_status.

Project Structure

druginteractions-kg/
├── etl/
│   ├── helpers.py              # Registry, batch ops, escaping
│   ├── download_data.py        # Bulk downloads with resume
│   ├── loader.py               # Orchestrator (4 phases)
│   ├── drugbank_dgidb_loader.py
│   ├── sider_loader.py
│   ├── chembl_ttd_loader.py
│   └── openfda_loader.py
├── mcp_server/
│   ├── config.yaml             # 12 domain tools
│   └── server.py
├── tests/
│   ├── test_helpers.py
│   ├── test_drugbank_dgidb_loader.py
│   ├── test_sider_loader.py
│   ├── test_chembl_ttd_loader.py
│   └── test_openfda_loader.py
├── schema/
│   └── druginteractions_kg.cypher
└── docs/
    └── druginteractions-kg-plan.md