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yeyuan98

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

gene_enrich

Read-only

Identify over-represented Reactome pathways from a list of at least three genes, with matched submitted gene counts per pathway.

Instructions

Perform pathway enrichment analysis for a gene list (Reactome over-representation). Requires at least 3 genes; the list is deduplicated (case-insensitive) before submission. Each pathway reports genes_overlap — the count of unique SUBMITTED genes Reactome matched there, resolved with one follow-up token lookup (Reactome's entity-level match count can exceed the gene count when one gene maps to multiple entities, e.g. a UniProt entry plus Ensembl gene/transcript). The reply also reports how many pathways Reactome found in total alongside the returned page. Typical completion is 15–45 s (the Reactome analysis takes 8–22 s per step across two sequential steps), with a worst case around 105 s including one retry per step; requires reachability of reactome.org, and clients whose request timeout is 60 s may need to raise it for large result follow-ups.

Input Schema

NameRequiredDescriptionDefault
genesYesList of HGNC gene symbols (minimum 3; duplicates and case variants are collapsed before submission)
limitNoMaximum pathways to return (1-100; Reactome reports up to ~100)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed3 schema fields changedv1.6.0-alpha.2
    • changedInput schema / properties / genes / description
      Previous value: -"List of HGNC gene symbols"New value: +"List of HGNC gene symbols (minimum 3; duplicates and case variants are collapsed before submission)"
    • addedInput schema / properties / genes / minItems
      Added value: +3
    • addedInput schema / properties / limit
      Added value: +{
+  "default": 30,
+  "description": "Maximum pathways to return (1-100; Reactome reports up to ~100)",
+  "maximum": 100,
+  "minimum": 1,
+  "type": "integer"
+}
  3. First observedv0.1.8

TDQS

A4.4/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Goes well beyond the readOnlyHint annotation: discloses deduplication behavior, how genes_overlap is resolved via a follow-up entity lookup and why it can exceed the submitted gene count, expected latency (15–45 s, worst case ~105 s with retries), external reachability of reactome.org, and a concrete client-timeout caveat. This is exactly the operational context annotations cannot convey.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the purpose and hard requirement, then layers operational detail. It is long and somewhat run-on in the genes_overlap and timeout sentences, but nearly every clause carries useful information, so waste is minimal.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description compensates by explaining return semantics (genes_overlap count, total pathways found vs. returned page) and the two-step timing profile. An agent has enough to call it correctly and set expectations for latency and result interpretation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% and the schema already documents both parameters, including the min-3 rule, dedup behavior, and the 1–100 limit range. The description restates the gene-list constraints without adding new syntax or format guidance, so baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Perform pathway enrichment analysis for a gene list') and names the underlying method (Reactome over-representation), which distinguishes it from the many gene_* retrieval siblings like gene_diseases or gene_drugs.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives clear preconditions for use — at least 3 genes, list deduplicated case-insensitively — and implies the scenario (you have a gene list and want pathways). It does not name an alternative tool or say when not to use it, so it stops short of the top score.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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