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Biotope

CLI integration for BioCypher ecosystem packages

Biotope is still under development

Biotope is still under development and the API is subject to change. The package is currently only meant for developer use and prototyping.

The Biotope CLI integration is our attempt to integrate BioCypher ecosystem packages into an accessible suite for scientific knowledge management. We are first approaching the project from a CLI perspective, as this is the most basic technology for prototyping automated workflows. We aim to extend this towards other user-interfaces, such as web apps, in the future.

Biotope contains various modules for different tasks, some of which are straightfoward applications of existing BioCypher packages, while others are prototypes for new features. See more information in the API documentation.

  • biotope init: Initialize a new project in the BioCypher suite
  • biotope build: Build a BioCypher knowledge representation
  • biotope chat: Chat with a BioCypher project (BioChatter)
  • biotope read: Extract information from unstructured modalities (BioGather)
  • biotope view: Use visual analysis tools to interpret your data and metadata
  • biotope get: Download files and automatically start annotation
  • biotope annotate: Annotate your data with consistent metadata in Croissant ML

Metadata annotation using Croissant, short guide

The biotope package features a metadata annotation assistant using the recently introduced Croissant schema. It is available as the biotope annotate module. Usage:

pip install biotope
biotope annotate interactive

You can also use the biotope get command to download files and automatically start the annotation process:

biotope get https://example.com/data/file.txt

This will download the file and pre-fill metadata fields based on the file's properties.

After creation, biotope can also be used to validate the JSON-LD (CAVE: being a prototype, biotope does not yet implement all croissant fields):

biotope annotate validate –jsonld <file_name.json>

biotope also has the method biotope annotate create to create metadata files from CLI parameters (no interactive mode) and biotope annotate load to load an existing record (the use of this is not well-defined yet). Further improvements would be the integration of LLMs for the automation of metadata annotations from file contents (using the biochatter module of biotope).

Unit tests to inform about further functions and details can be found at https://github.com/biocypher/biotope/blob/main/tests/commands/test_annotate.py and https://github.com/biocypher/biotope/blob/main/tests/commands/test_get.py

  • Copyright © 2025 Sebastian Lobentanzer.
  • Free software distributed under the MIT License.