BioCypher
Community
Docs:
BioCypher
BioChatter
Biotope
Initializing search
biocypher/biocypher
Home
About
BioCypher
BioChatter
Biotope
Community
BioCypher
biocypher/biocypher
Home
About
About
Overview
Philosophy
Timeline and Publications
Sponsors
Community
Community
User workshop 2026
Join Us
Where to Start
Contribute to the Documentation
Contribute to the Code Base
BioCypher
BioCypher
Home
About
About
Project
Design philosophy
Use Cases
BioCypher + LLMs
R and Bioconductor
Get Started
Get Started
Installation
Quickstart
LLM Integration
Learn
Learn
Overview
Tutorials
Tutorials
Overview
Catalog by Level
Python UI track
Python UI track
Hands-on Protein Graphs with BioCypher and Neo4j (Beginner)
Handling Ontologies (Intermediate)
Data harmonization and merging (Advanced, planned)
LLM-assisted UI track
LLM-assisted UI track
Agent-supported hands-on Protein Graphs with BioCypher and Neo4j (Beginner)
Agent API (Beginner)
OntoWeaver track
OntoWeaver track
OntoWeaver Tutorial (Beginner)
HowTo / FAQ
HowTo / FAQ
Overview
Connect the MCP to your IDE
Standalone Docker Image
Large-scale Offline Builds
Explanations
Explanations
Overview
Knowledge Graphs
Ontologies
Knowledge Graphs in BioCypher
Adapters
Schema Configuration Philosophy
Graph Class Guide
Architecture Migration Guide
Reference
Reference
Reference Index
API Documentation
API Documentation
API Reference
BioCypher
BioCypherWorkflow
Graph Class
Output Writing
Output In-Memory
Output Driver
Download and Cache
Ontology Handling
Graph Handling
Mapping and Translation
Logging
Miscellaneous Utility Functions
BioCypher Configuration
Output Configuration
Output Configuration
Overview
Neo4j
SQLite
PostgreSQL
NetworkX
Tabular Format
RDF
OWL
ArangoDB
Schema Configuration
Community
Community
Join Us
Where to Start
Contribute to the Documentation
Contribute to the Code Base
BioChatter
BioChatter
Home
About
About
Project
Design Philosophy
Use Cases
Get Started
Get Started
Installation
Quickstart
Learn
Learn
Tutorials
Tutorials
Basic Usage - Chat
Multimodal Models
Retrieval-Augmented Generation
In Chat Tool Calling
Ad hoc API Calling
Structured outputs
Reflexion via LangGraph
Open-source and Local LLMs
The Living Benchmark
Podcast my Paper
LLM in your Browser - WebAssembly
HowTo / FAQ
HowTo / FAQ
Knowledge Graph RAG
Retrieval-Augmented Generation (RAG)
Customising BioChatter Light - Simple
Customising BioChatter Light - Advanced
Customising BioChatter Light and Next - Cancer Genetics Use Case
Benchmark
Benchmark
Overview
All Results
Developer Guide
Reference
Reference
API Documentation
API Documentation
LLM Connectivity
Vectorstore Agent
Knowledge Graph Agent
API Calling: Base Classes
API Calling: Web APIs
API Calling: Python APIs
Reflexion Agent
Podcast
Biotope
Biotope
Home
Tutorial
Plugin & Skills
Commands
Mapping
How it works
Cluster compliance
Community
Knowledge Graphs in BioCypher