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| Meta |      |
| Automation |
CLI integration for BioCypher ecosystem packages
Status: early alpha, volatile
Currently discussed here
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
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). Obvious improvements would be to integrate file download (something like biotope annotate get) with automatic annotation functionalities, and the integration of LLMs for the further 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
- Copyright © 2025 Sebastian Lobentanzer.
- Free software distributed under the MIT License.