biotope

Build a knowledge graph from data files using biotope, the CLI for the BioCypher ecosystem (Croissant-described data → BioCypher graph, with git-like metadata version control). Use this whenever the task is to turn tables, CSVs, JSON, parquet, or mixed/unstructured sources into a queryable knowledge graph or graph database (Neo4j, DuckDB) — including ingesting a dataset into a graph, mapping fields to entities and relations, building a BioCypher project, connecting biomedical/biological data across sources, or grounding data against ontologies. Trigger on mentions of biotope, BioCypher, Croissant, knowledge graph / KG construction, graph ingestion, "turn this data into a graph", entity/relation mapping, or ontology-grounded data integration — even when the user names the goal (a graph) rather than the tool.

Connect biomedical LLM chat to knowledge graphs, APIs, and document RAG with BioChatter. Use for natural-language Cypher over Neo4j, BioCypherPromptEngine query generation, DatabaseAgent, or general biomedical conversation with structured backends. Trigger on BioChatter, NL graph queries, Cypher generation, KG chat, schema_info.yaml querying, or conversational AI over biomedical data.

Build knowledge graphs with BioCypher — adapters, schema_config.yaml, biocypher_config.yaml, and multi-backend export (Neo4j, CSV, PostgreSQL, RDF). Use for standalone KG ETL pipelines, writing schema_info.yaml, Neo4j bulk import, or tuning dbms/output settings. Trigger on BioCypher, schema_config, biocypher_config, write_nodes, write_edges, knowledge graph construction, Biolink schema, or graph database export.