Biotope

Biotope builds knowledge graphs from local data. It uses croissant-baker to describe sources, gives every described input a typed Python source package from the reviewed Croissant metadata, and checks project-owned loaders, mappings and graph pipelines. Builds export BioCypher files with provenance and a record of the run.

Biotope is under active development. The 0.10 release generates a complete source inventory, reports source drift, and retires validation checks and the query context; see the migration guide.

Install

Use Python 3.10–3.12. These commands use uv and a POSIX shell:

uv venv --python 3.12 .venv
uv pip install --python .venv/bin/python 'biotope[graph]>=0.10,<0.11'
source .venv/bin/activate
biotope --version

This installs the published croissant-baker dependency automatically. Graph type checking also needs Node.js on PATH; alternatively, install pyright[nodejs] in this environment. See installation for other setups.

Build a graph

1. Initialize a metadata project with biotope init my-kg, then enter my-kg.
2. Describe selected local data with biotope add <path> and review the Croissant metadata.
3. Run biotope graph scaffold, then give every described input a source package with biotope source generate <manifest> --out graph/sources.
4. Select or exclude each source, then define the graph's schemas, loaders, topology, mappings and pipeline in Python.
5. Run biotope graph check, then biotope graph build, which writes graph/build/.
6. Review the exported values, descriptions and provenance against the research question, reading the sources themselves; checks establish structure, not scientific correctness.

The scaffold's README describes its layout. The tutorial provides a complete synthetic project you can run immediately.

• Typed graph guide: source curation, authoring and review.
• Commands: metadata, graph and version-control workflows.
• Architecture: responsibilities and execution boundaries.
• Published documentation.

Use with a coding agent

The repository includes a biotope-croissant skill for this workflow and a biocypher skill for standalone BioCypher projects. Follow the agent setup guide for Claude Code, Cursor or Codex. Skills guide the agent; install the Python package in the project environment too.

Contribute

See CONTRIBUTING.md for development setup, checks and release conventions. Report reproducible problems through GitHub issues.

Typed authoring and modular topology construction were informed by Paul Ka Po To's kg-build-system. Biotope does not depend on that engine.

Copyright © 2025–2026 BioCypher Team. Apache 2.0.