biotope

Turn tables, CSVs, and mixed biomedical data into a queryable knowledge graph, with version-controlled metadata.

Pre-alpha

CLI flags and APIs will change. The plugin skills are the most stable onboarding path.

Start with a coding agent

Install the biotope plugin, then invoke /biotope-croissant or ask:

What does biotope do? I want to build a graph from my data.

The agent asks what the graph should answer and runs the pipeline:

init → add → map → build → view

Semantic choices stay with you or your agent. Biotope inspects, validates, and previews; it never guesses the best record set or field mapping.

Use the CLI

For manual or scripted use:

Try without installingInstall globallyAdd to a uv project

uvx biotope init my-kg

pipx install "biotope>=0.8.0"

uv add "biotope>=0.8.0"

Next:

• Build an airport graph in about 15 minutes.
• Use the command overview for manual work and scripts.
• Write mappings by hand with the mapping reference.
• Read how biotope works for project layout and data flow.