Reproduce Paper Workflows with Skills

BioMCP paper demos are consolidated into embedded skill workflows so any agent can run them without a custom runtime. Use this guide to map each paper-style task to the canonical skill and execution pattern.

Mapping

Paper-style workflow	Canonical skill	Typical command
GeneGPT	09-gene-function-lookup	biomcp skill gene-function-lookup
GeneAgent	10-gene-set-analysis	biomcp skill gene-set-analysis
TrialGPT	03-trial-searching (patient matching section)	biomcp skill 03
PubMed & Beyond	11-literature-synthesis	biomcp skill literature-synthesis

Basic Flow

1. List available workflows.
2. Retrieve one by number or slug.
3. Execute the included CLI steps.
4. Verify results against that skill's validation checklist.

biomcp skill list
biomcp skill gene-function-lookup

Suggested Execution Pattern

For a reproducible run, copy command output to a markdown log and keep IDs (PMIDs/NCT IDs) visible in the final summary.

biomcp skill 10
biomcp enrich "BRCA1,TP53,ATM,CHEK2,PALB2" --limit 10
biomcp get gene BRCA1 pathways

Notes

• Skills are model agnostic; any shell-capable agent can execute them.
• If a service is temporarily rate limited, retry after a short pause.
• If enrichment is unavailable, continue with pathway/interaction/literature verification steps in skill 10.