Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/lucas-servi/kegg-mcp-server-python/kegg-analysisnpx skills add Lucas-Servi/kegg-mcp-server-python --skill kegg-analysisgit clone --depth 1 https://github.com/Lucas-Servi/kegg-mcp-server-pythonWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/lucas-servi/kegg-mcp-server-python/kegg-analysis)<a href="https://agentmods.dev/skills/lucas-servi/kegg-mcp-server-python/kegg-analysis"><img src="https://agentmods.dev/badge/skills/lucas-servi/kegg-mcp-server-python/kegg-analysis.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00098 | $0.01492 |
| Opus 5 | $0.00049 | $0.00746 |
| Sonnet 5 | $0.00020 | $0.00298 |
| Haiku 4.5 | $0.00010 | $0.00149 |
Grade A, and why
kegg-analysis scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.
KEGG Bioinformatics Analysis
Guide the user through structured KEGG database queries using the kegg MCP server tools.
Available Tools
You have access to 34 KEGG tools via the kegg MCP server. Key categories:
| Category | Tools | Use for |
|---|---|---|
| Pathways | search_pathways, get_pathway_info, get_pathway_genes, get_pathway_compounds, get_pathway_reactions |
Finding and exploring metabolic/signaling pathways |
| Genes | search_genes, get_gene_info, get_gene_orthologs |
Gene function, cross-species orthologs |
| Compounds | search_compounds, get_compound_info, get_compound_reactions |
Metabolites, substrates, products |
| Reactions | search_reactions, get_reaction_info |
Biochemical transformations |
| Enzymes | search_enzymes, get_enzyme_info |
EC numbers, catalytic activity |
| Diseases | search_diseases, get_disease_info |
Disease-gene-drug associations |
| Drugs | search_drugs, get_drug_info, get_drug_interactions |
Pharmacology, DDI |
| Orthology | search_ko_entries, get_ko_info |
Functional orthologs (KO) |
| Cross-DB | batch_entry_lookup, convert_identifiers, find_related_entries |
Bulk queries, ID mapping (UniProt, NCBI, ChEBI) |
| Visualization | render_pathway_ascii |
ASCII pathway diagrams |
Workflow Patterns
Pattern 1: Gene List → Pathway Enrichment
When the user provides a gene list:
- Identify the organism code (e.g.,
hsafor human,ecofor E. coli,scefor yeast) - For each gene, use
search_geneswith the organism to get KEGG gene IDs - For each gene ID, use
get_gene_infowithdetail_level="full"to get pathway associations - Tally pathway frequencies across the gene list
- For enriched pathways (appearing 2+ times), use
get_pathway_infoto describe their function - Summarize: which pathways are over-represented, what biological processes they reflect
Pattern 2: Pathway Deep Dive
When the user asks about a specific pathway:
- Use
search_pathwaysto find the pathway ID if not provided - Use
get_pathway_infowithdetail_level="full"for overview - Use
get_pathway_genes,get_pathway_compounds,get_pathway_reactionsfor components - Use
render_pathway_asciito visualize topology - Highlight key enzymes, rate-limiting steps, and regulatory points
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 6d ago First seen · 113 lines · 98 tokens per session scan A 4c2d867f76c8
kegg-analysis is a skill published in the GitHub repository Lucas-Servi/kegg-mcp-server-python (3 stars, last pushed 23d ago), licensed MIT. It adds 98 tokens to every session and 1,492 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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