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mcpbio_test MCP server · F · ToolBench

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mcpbio_test

github.com/ThomVett/mcpbio_test

Biomedical MCP server with KEGG pathway analysis and drug interaction lookup tools

2026-07-28+STDIO8 tools

42/100

Definition Quality50

Protocol Readiness50

Supportability23

Spec posture

Inferred effective spec 2026-07-28+·current baseline 2026-07-28

Static source inference · medium confidence

Current-spec patterns detected

Summary

Server has 8 tools with significant quality gaps. Tool naming is inconsistent (duplicate 'kegg_pathway_proteins' at indices 3 and 8). Descriptions are present but generic (avg ~60 chars, below 194-char baseline). Input schemas are visible and typed, but parameter descriptions are minimal. No output schemas documented. Error handling is absent, no recovery guidance or categorization. Tool composition mixes unrelated domains (KEGG biology + weather). Critical: descriptions lack WHEN/WHY context needed for LLM selection.

Tools (8)

check_drug_links_for_uniprot_idsread onlysource verified62/100

Looks up drug interactions for given UniProt protein IDs.

get_alertsread onlysource verified58/100

Get weather alerts for a US state.

get_forecastread onlysource verified58/100

Get weather forecast for a location.

get_pathway_proteins_from_keggread onlysource verified60/100

Retrieves protein information from KEGG pathways.

get_proteins_that_are_in_too_listsread onlysource verified50/100

Based on the two input protein lists returns the proteis that are present in the two protein lists

go_functional_similarityread onlysource verified53/100

Gets a list of genes that are similar to gene name according to their gene ontology

kegg_pathway_proteinsread onlysource verified60/100

Get proteins in a biological pathway from KEGG.

Issues (5)

CRITICALtool ↗

Duplicate tool registration: 'kegg_pathway_proteins' appears at indices 3 and 8 with identical schemas. This confuses LLM tool selection and violates single-responsibility principle.

kegg_pathway_proteins

HIGHtool ↗

Domain mismatch: KEGG biology tools (get_pathway_proteins, check_drug_links, go_functional_similarity) mixed with weather tools (get_alerts, get_forecast) in same server. LLM cannot infer coherent purpose.

get_alertsget_forecastget_pathway_proteins_from_kegg

HIGHtool-description ↗

Descriptions lack WHEN/WHY context. 'Retrieves protein information from KEGG pathways' does not explain when to call this vs check_drug_links_for_uniprot_ids or go_functional_similarity. LLMs cannot disambiguate.

get_pathway_proteins_from_keggcheck_drug_links_for_uniprot_idsgo_functional_similarity

HIGHresponse-shaper ↗

Recommendations

Remove duplicate 'kegg_pathway_proteins' tool (index 8). Keep only one canonical version with clear naming.
Split server into two: 'mcpbio' (KEGG/UniProt/drug tools) and 'mcpweather' (weather tools). Separate concerns enable focused LLM reasoning.
Expand tool descriptions to 100-200 chars. Add WHEN/WHY: 'Use this to find all proteins in a biological pathway (e.g., apoptosis) and map them to UniProt IDs for drug interaction lookup. Call this BEFORE check_drug_links_for_uniprot_ids.'
Document output schemas in tool definitions. Expose PathwayProteinResponse and DrugLookupResponse fields (pathway_id, proteins[], uniprot_id, etc.) so LLMs know what to extract.
Add timeout (5s), retry logic (3 attempts), and user-actionable error messages. E.g., 'KEGG API timeout. Try again in 30s or use a different pathway name.' instead of silent failure.

Score history

Overall score trend

First recorded score · v2 rubric

42/100

Scored	Grade	Overall	Spec posture	Rubric
2026-09-23	F	42	2026-07-28+	v2