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Commands

biotope --help lists command groups. Run biotope <command> --help for current flags and examples. This page shows how commands fit into the pipeline.

Project lifecycle

  • biotope init: scaffold a project (.biotope/, project.yaml, git init).

Data acquisition and tracking

  • biotope get <url>: download a file, optionally into --output-dir, and track it unless you pass --no-add.
  • biotope add <path>: stage data files or rooted directories. Baker writes Croissant metadata under .biotope/datasets/. --derived-from records provenance for extracted files. For metadata that does not fit in CLI flags, such as citations or per-record-set fields, add also writes a .biotope.yaml scaffold next to the dataset. Review it, then run biotope annotate apply <dir> to merge it into the manifest.
  • biotope mv / biotope rm: move or untrack files and update metadata paths.
  • biotope queue: group every dataset by pipeline state (raw, processed, or mapped). Use it as the dashboard during a build.
  • biotope mark <dataset> <status>: set a dataset's biotope:status manually.

Semantic mapping

For the mapping YAML grammar and reliability rules, see the mapping reference.

  • biotope map: update project.yaml non-interactively when passed intent flags (--purpose, --entity, --relation, --source, --notes, --clear-*, or --show). With no flags, it opens the guided wizard.
  • biotope map inspect <croissant>: list fields and sample rows. Pass --json for machine-readable output.
  • biotope map scaffold <croissant>: write an unresolved mapping scaffold with the inspection results in a comment appendix.
  • biotope map preview [<mapping>]: validate a partial mapping and show its projected BioCypher schema and sample tuples. Pass --json for agents.
  • biotope propose-alignment: propose cross-mapping same_node equivalences.

Git-like metadata VCS

  • biotope status: show staged or modified files and validation state.
  • biotope commit: commit metadata changes.
  • biotope log: show metadata commit history.
  • biotope push / biotope pull: sync metadata with a remote.
  • biotope check-data: verify data files against recorded checksums.

Knowledge-graph construction

  • biotope build: create a runnable BioCypher project from mappings and alignment. It writes config/schema_config.yaml and generated Python for each mapping under build/generated/<stem>/.
  • biotope view: show node and edge counts for the latest build, or project competence questions before the first build.

Annotation and project configuration

  • biotope annotate: apply or edit metadata, load sample records, and validate manifests. apply accepts --set dataset.<field>=... and --set record_set.<field>=... overrides.
  • biotope config: manage validation rules, remote validation URLs, and project metadata.

Not yet implemented

  • biotope discover: rank registered adapters and local Croissant files against required_entities. The registry is not part of the recommended workflow yet.
  • biotope benchmark: emit a skeleton metrics object for downstream tests. Quality and coverage metrics are not implemented yet.
  • biotope read: reserved for NLP ingestion. It currently provides a health check only.
  • biotope search: search MCP and bio.tools registries. The standard build path does not use it.

Deprecated

  • biotope describe: removed. Use the intent flags on biotope map.
  • biotope propose-mapping: deprecated alias for biotope map scaffold. It writes an unresolved scaffold for a human or agent to complete.