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三域医研 · 科研算法引擎 (SanYu Research Engine)

GO / KEGG enrichment / 通路富集(GO/KEGG)

go_kegg_enrichment
Read-only

GO / KEGG enrichment / 通路富集(GO/KEGG) | USE WHEN: pathway enrichment for a gene list (GO biological process, KEGG) | ALIASES: 富集分析, GO, KEGG, 通路富集, enrichment, 通路, 功能注释 | RETURNS: 富集通路与 P 值

Example tool call

This call uses example arguments supplied in the tool’s input schema.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "db_filter": "KEGG",
      "gene_list": [
        "TP53",
        "EGFR",
        "MYC",
        "KRAS",
        "BRCA1"
      ]
    },
    "name": "go_kegg_enrichment"
  }
}

Input Schema

NameRequiredDescriptionDefault
db_filterNo数据库:GO_BP/GO_CC/GO_MF/KEGG
gene_listYes基因列表
project_idNo项目 id

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered by structured data. The description adds only a light return hint ('富集通路与 P 值'), and says nothing about the statistical procedure, multiple-testing correction, background gene set, or species assumptions, all of which materially affect interpretation of an enrichment result.

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

Conciseness3/5

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

The pipe-delimited layout is front-loaded with the actionable USE WHEN clause, which is good. However, the ALIASES line is keyword padding ('富集分析, 通路, 功能注释') that conveys no operational information, and the title is duplicated twice as the first segment and the title field.

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

Completeness3/5

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

For a read-only, single-required-parameter tool with no output schema, the description covers purpose and a rough return shape. It omits what an agent most needs before calling: expected gene identifier format (symbol vs. Entrez), organism scope, and how P values are adjusted, which are common failure points for enrichment tools.

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 description coverage is 100%, and each of the three parameters (db_filter, gene_list, project_id) is already documented in the schema, including the GO_BP/GO_CC/GO_MF/KEGG vocabulary. The description mentions the gene list but adds no format or identifier-convention detail, so the baseline 3 applies.

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

Purpose4/5

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

The title line and the USE WHEN clause state a specific verb and resource: pathway enrichment (GO biological process / KEGG) over a supplied gene list. An agent can tell what it produces, but the description never distinguishes it from nearby siblings such as protein_enrichment, gene_pathway_disease, or metabolite_pathway, so the boundary is left to inference.

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?

The 'USE WHEN: pathway enrichment for a gene list' clause gives a clear triggering condition, which is the main routing cue an agent needs. It stops short of exclusions or named alternatives, so 5 is not warranted.

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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