BioCypher

Open infrastructure
for biomedical
data management.

The BioCypher ecosystem brings together open, community-driven tools for dependable biomedical knowledge management.

BioCypher is published in Nature Biotechnology. Read the BioCypher paper →

A community of partners and users.

  • Helmholtz Munich
  • EMBL-EBI
  • Heidelberg University
  • TomTom
  • Open Targets
  • Institut Pasteur
  • Harvard Medical School
  • IggyTop
  • ELIXIR
  • DFG
  • IGVF
  • OptimusKG
  • Stanford University
  • Metalinks

Home

Why the BioCypher ecosystem

One workflow, from raw data to grounded answers

Each step uses your project's context to stay focused and semantically grounded.

Gather

Pull in data from any source. Extract structured entities from text and messy files, annotated with portable metadata.

Biotope BioCroissant

Build

Construct ontology-aligned knowledge graphs with reusable adapters, and export the same build to different formats and environments.

BioCypher

Reason

Query and chat with your graph. Connect it to LLMs and shared context resources for grounded, agentic analysis.

BioChatter BioContext
Read more about the ecosystem.

Ecosystem publications

Core publications from the BioCypher ecosystem

Deployed use cases

BioCypher in scientific knowledge-graph projects.

Regulatory genomics · Stanford / ENCODE

IGVF Catalog / ENCODE

BioCypher helps the IGVF team shape genomic variation data into a Biolink-inspired graph with a user-facing API.

 Plant biology · RWTH Aachen

TomTom knowledge graph

TomTom uses BioCypher to integrate tomato multi-omics data for gene and protein function discovery.

 Metabolism · Heidelberg

Metalinks

BioCypher reduced the first structured knowledge-graph build from about 2.5 months of scripts to roughly two weeks.

Community

Ways to join

Use the tools, cite the papers, ask questions, or contribute code and docs.

Contribute on GitHub

Report issues, improve adapters, add documentation, or review open pull requests.

Open GitHub →

Activity

Recent work

Workshops, BioHackathons, releases, papers, and related tools from the BioCypher community.

BioCypher workshop participants
June 2026 · Workshop

Building the biomedical KG community

User workshop on shared knowledge-graph practice in biomedical science.

2026

Biomedical KG community workshop User workshop focused on shared practices. TomTom knowledge graph Integrated tomato knowledge graph published in New Phytologist. IggyTop release Immune receptor signalling knowledge graph released. Agentic Automation Canvas Double-feature preprint on agentic automation and expectation gaps.

2025

Systems biology model loading ELIXIR BioHackathon Germany contributions to BioCypher and BioChatter. BioContext in Nature Biotechnology BioContext paper published and the registry launched at biocontext.ai. EDAM Ontology MCP server ELIXIR BioHackathon Europe contributions to biomedical MCP infrastructure. Medical benchmarking study Published in npj Digital Medicine.