Graffold

Knowledge graph platform for protein-disease relationships. Turns biomedical literature and datasets into a queryable, semantically-rich graph (Neo4j or Memgraph).

Getting Started

• Quick Start — Install, configure, and run your first query
• Knowledge Graph Creation Guide — End-to-end workflow for building production KGs
• Hetzner Operations — Deployment, monitoring, and maintenance

Product Specs

• Enterprise Drive Graph and Dataset Harmonization Workbench — PRD for refactoring the API and frontend around cloud-drive file-system graphs and dataset harmonization
• Drive Graph API Implementation — Backend requirements for workspaces, drive sources, crawls, artifacts, graph search, review decisions, and reports

Architecture

• Architecture Diagrams — Mermaid diagrams: query pipeline, security flow, evaluation framework, end-to-end sequence
• Technology Stack — Complete technology catalog organized by domain
• Orchestration & Agents — Agent architectures, LangChain tools, query classification, MCP server
• Security Guardrails — Prompt injection, Cypher injection, PII detection, defense-in-depth
• Semantic Dynamic Context Graph — Provenance, temporal validity, user context
• Query Agents — Agent types, search strategies, and routing

Ingestion & Enrichment

• Entity Consolidation — UniProt IDs, synonym matching, MONDO ontology
• Incremental PubMed Updates — Weekly maintenance workflow
• PDF Extraction Setup — MarkItDown, Nougat, pdftotext
• Relationship Extraction — Confidence scoring, evidence tracking
• Node Management — Node labeling, type resolution
• PPI Framework — Protein-protein interaction data model
• Multi-Source PPI Guide — Combining multiple sources

Querying

• GFQL Patterns — Graph Foundation Query Language patterns
• KG Tools Guide — Tool registry and MCP adapter
• Multi-Hop Traversal — Deep graph exploration
• Evidence Weighting — Confidence scoring and ranking
• Test Query Set — Validation queries

Operations

• Redis Integration — Distributed caching setup
• Grafana Dashboard — Metrics, alerting, and dashboards
• Metrics Dashboard — Unified performance metrics

Development

• Testing Guide — Test framework, markers, and conventions
• CLI & TUI — Command-line interface documentation
• API Reference — REST API endpoints and models