Metabolomics Annotation

Example Queries

• "Annotate these metabolomics features using SIRIUS"
• "Match MS2 spectra against GNPS libraries"

Output Structure

output_directory/
├── report.md
├── result.json
├── annotated.csv
├── figures/
│   └── chemical_class_distribution.png
├── tables/
│   └── compound_identifications.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Local database matching where possible; transparent interactions for external APIs (like GNPS).
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• peak-detection — Upstream feature extraction
• met-diff — Downstream structural interpretation of significant hits

Citations

• SIRIUS
• GNPS
• MetFrag