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:
- Column re-scan for disease-related field names
- LLM-based abstract extraction from publication context
- LLM-based methods section parsing
- 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
1 maintainer
Metadata
1 maintainer
Release files for lobster-metadata 1.1.426
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