Pharma Wiki — Knowledge Graph Skill

Build a persistent, compounding pharmaceutical knowledge base with structured entity/relation extraction, normalization, and interactive graph visualization.

Architecture

Three layers under a project root:

• raw/ — Immutable source documents (markdown)
• wiki/ — Human-readable compiled articles + index + log
• graph/ — Structured knowledge graph (JSON):
  • entities.json — All entities with aliases, types, descriptions
  • relations.json — All binary relations (triples)
  • viz.html — Auto-generated interactive D3.js visualization

Entity Types (12 + Other)

Drug, Target, Disease, Gene, Protein, Pathway, AdverseEvent, ClinicalTrial, Biomarker, Dosage, Contraindication, Mechanism