Plugin and skills
The biotope plugin teaches coding agents how to run the knowledge-graph
pipeline. The agent uses the same biotope CLI as a human; no separate agent
API or MCP server is involved.
Install
Add a team marketplace
and import biocypher/biotope.
Add a marketplace from the CLI
using https://github.com/biocypher/biotope.
To install skills without the plugin, copy the folders you need from
skills/ into your
agent's skills directory, such as .cursor/skills/ or .claude/skills/.
Choose a skill
| Skill | Use it for |
|---|---|
biotope-croissant |
Build a graph from data: init → add → map → build |
biocypher |
Configure export backends, schemas, and Neo4j import |
biochatter |
Query a loaded graph in natural language |
Start with biotope-croissant. Add the other skills when the pipeline reaches
those stages.
Work with the agent
Invoke /biotope-croissant to load the skill, or just describe the goal and
let the agent trigger it:
Turn the CSVs in
data/into a knowledge graph of genes and diseases.
The skill drives the CLI for you. During a typical session:
- The agent asks what the graph should answer and which entities and relations matter. It records your answers as the project purpose instead of guessing from file shapes.
- It brings your data into the project and runs
add, which creates a Croissant manifest for each dataset. - It writes one mapping per dataset and previews each edit. A clean preview does not guarantee a connected graph, so this may take several passes.
- It builds the graph and checks node counts, edge counts, and orphaned edges before reporting success.
The agent asks before choosing the graph's purpose, extracting facts from
unstructured files, selecting csv or neo4j, or changing the declared
schema.
When the pipeline reaches export tuning or querying, the agent switches to the
matching skill: biocypher for Neo4j import and schema config, biochatter
for natural-language queries.
To write mappings yourself, see the mapping reference. For a full worked example, follow the tutorial.
Agents without skills
biotope init --agents-md adds a project-local AGENTS.md fallback. Use it
only when your agent cannot load skills.