lobster-metadata 1.1.411

Metadata assistant agent for Lobster AI - sample metadata and harmonization operations

lobster-metadata

Sample metadata management and harmonization for multi-omics datasets.

Installation

pip install lobster-metadata

Agents

Agent	Description
metadata_assistant	Metadata operations specialist. Sample ID mapping, schema standardization, dataset validation, and disease annotation enrichment.

Services

Service	Purpose
SampleMappingService	Map sample IDs between datasets using multiple strategies
MetadataStandardizationService	Standardize metadata fields to Pydantic schemas
MetadataFilteringService	Filter datasets by metadata criteria
DiseaseStandardizationService	Standardize disease names to controlled vocabularies
DiseaseOntologyService	Map diseases to ontology terms (MONDO, DO)
ClinicalMetadataService	Extract and validate clinical metadata fields
SampleGroupingService	Group samples by metadata attributes
MicrobiomeFilteringService	Microbiome-specific metadata filtering

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