BASALT

Broad Analytical Schema for Samples and Laboratory Techniques

LinkML schema for MONet/EMSL scientific data across biogeochemical, biological, and environmental domains. Canonical source of truth for samples, provenance, laboratory activities, and analytical products used by the Analysis API and database models.

Formerly analysis-api-schema.

Schema version	0.1.0 (see version in basalt_schema.yaml)
Package	basalt_schema (Python package version follows git tags via uv-dynamic-versioning)
Docs	https://EMSL-Computing.github.io/basalt-schema
Repository	https://github.com/EMSL-Computing/basalt-schema
Canonical URI	https://EMSL-Computing.github.io/basalt-schema

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • basalt_schema
    • schema -- LinkML schema
    • datamodel -- generated
• tests/ - Python tests
• util/ - Adhoc LinkML replacement code

Versioning

BASALT uses semantic versioning (MAJOR.MINOR.PATCH) for the schema:

Change type	Bump	Examples
MAJOR	Breaking model changes	Rename/remove classes or required slots; change identifiers; incompatible range changes
MINOR	Backward-compatible additions	New optional classes/slots/enums; new modules; expanded permissible values
PATCH	Non-breaking fixes	Description/docs fixes; typo corrections; generator/tooling-only fixes that do not change the model

How versions are recorded

1. Schema version (authoritative for the data model)
   Set in the root schema file:

   # src/basalt_schema/schema/basalt_schema.yaml
   version: 0.1.0

2. Python package version
   Derived from git tags (v0.1.0, v0.2.0, …) via uv-dynamic-versioning.
   Installable package name: basalt_schema.

Developer Documentation

uv sync
just gen-project

Windows and PowerShell users can use the same commands when uv and just are installed.

Credits

This material is free to use, and attribution is always appreciated. Attribution may read as follows:

Authored by Conrad Mearns, Maia Kapur, Montana Smith, Beata Meluch, Aramy Truong, and Yuri E. Corilo at the Pacific Northwest National Laboratory, operated by Battelle for the U.S. Department of Energy.

Please cite the following in your work:

Prymolennna, A., Zalmanek, B., Kapur, M. S., Meluch, B. J., Smith, M., Mearns, C., Truong, A.& Corilo, Y. (2026). EMSL-Computing/BASALT-Schema: v0.1.0 — Initial public release of BASALT schema (Version v0.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.21893602