lobster-metadata

Sample metadata management and harmonization for multi-omics datasets.

Installation

pip install lobster-metadata

Agents

Services

Features

Sample ID Mapping

• Exact match between matrix and metadata identifiers
• Fuzzy matching with configurable similarity thresholds
• Pattern-based matching using regular expressions
• Metadata-based correlation for complex mapping scenarios

Metadata Standardization

• Transcriptomics schema (cell type, tissue, organism, disease)
• Proteomics schema (platform, quantification method, normalization)
• Microbiome schema (16S vs shotgun, taxonomic level, diversity)

Dataset Validation

• Sample count consistency between matrix and metadata
• Condition coverage verification for experimental design
• Control sample identification and validation
• Biological and technical replicate detection
• Platform consistency checks across samples

Disease Enrichment

Four-phase hierarchy for missing disease annotations:

1. Column re-scan for disease-related field names
2. LLM-based abstract extraction from publication context
3. LLM-based methods section parsing
4. Manual mapping fallback for known datasets

Multi-Omics Integration

• Cross-modality sample alignment
• Shared sample identification across data types
• Metadata merging with conflict resolution

Requirements

• Python 3.12+
• lobster-ai >= 1.0.0

Testing

To run the test suite for this package:

# Install in editable mode with dev dependencies
pip install -e ".[dev]"

# Run all tests
pytest tests/ -v

# Run specific test categories
pytest tests/services/metadata/ -v  # Service tests only
pytest tests/agents/ -v             # Agent tests only

Documentation

Full documentation: docs.omics-os.com/docs/agents/metadata

License

AGPL-3.0-or-later