| name | proteomics-enrichment |
| description | Pathway, network, and functional enrichment for proteomics using STRING, DAVID, or g:Profiler. |
| version | 0.1.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["proteomics","enrichment","pathway","STRING","g:Profiler"] |
| metadata | {"omicsclaw":{"domain":"proteomics","emoji":"🗺️","trigger_keywords":["proteomics enrichment","pathway analysis","STRING","DAVID","g:Profiler","GO enrichment"],"allowed_extra_flags":["--method","--species"],"legacy_aliases":["prot-enrichment"],"saves_h5ad":false}} |
🗺️ Proteomics Enrichment
Pathway, network, and Gene Ontology enrichment analysis for proteomics data.
CLI Reference
python omicsclaw.py run prot-enrichment --demo
python omicsclaw.py run prot-enrichment --input <proteins.csv> --output <dir>
Parameters
| Parameter | Default | Description |
|---|
--method | ora | ora or gsea |
--species | human | Species |
Why This Exists
- Without it: A list of 500 significant proteins is biologically impossible to interpret
- With it: Algorithms collapse hundreds of targets into 5 or 10 meaningful biological pathways
- Why OmicsClaw: Runs fast local enrichment caches utilizing multiple ontologies simultaneously
Workflow
- Calculate: Map Uniprot IDs to Gene Symbols or Entrez.
- Execute: Hypergeometric tests over known Kegg/GO definitions.
- Assess: Perform FDR multiple testing adjustments.
- Generate: Output structural network graphs.
- Report: Tabulate key functionally enriched terms.
Example Queries
- "Perform GO enrichment on these significant proteins using STRING"
- "Run g:Profiler on this list of genes"
Output Structure
output_directory/
├── report.md
├── result.json
├── pathways.csv
├── figures/
│ └── enrichment_dotplot.png
├── tables/
│ └── top_pathways.csv
└── reproducibility/
├── commands.sh
├── requirements.txt
└── checksums.sha256
Safety
- Local-first: Strict offline processing without external upload.
- 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:
differential-abundance — Upstream source of significant proteins
Citations
