Public omics metadata harmonization

omicsmeta

Harmonize public omics metadata from GEO, SRA, BioSample, and tabular exports with domain-specific normalization, ontology mapping, and reviewable output tables.

Start with the CLI Read the design

Current Scope

The package is currently pre-alpha. The documentation describes implemented behavior and calls out limitations where the roadmap is not complete.

Run metadata harmonization Install from PyPI, harmonize local files, and export mapped and unmapped review tables. Use the Python API Call the harmonizer directly from scripts and notebooks with row dictionaries. Inspect pipeline decisions Understand field detection, mapper routing, validation, and output semantics. Benchmark known answers Run the bundled fixture and compare observed mappings to expected ontology IDs.

Start Here

• Quickstart: install the package and run the CLI.
• API reference: call the harmonizer from Python.
• Design: understand pipeline decisions and output semantics.
• Release readiness: validate artifacts and release claims before publishing.
• Basic fixture tutorial: run the local example and benchmark it against known-answer mappings.