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Lucas-Servi

kegg-mcp-server

by Lucas-Servi

render_pathway_ascii

Read-onlyIdempotent

Convert KEGG pathway data into ASCII representation for machine reading. Linear chain style shows reaction sequences; grid style displays spatial layout.

Instructions

Render a KEGG pathway as ASCII text optimized for LLM consumption.

Two styles available:

  • 'chain': Linear reaction flow text showing substrate->enzyme->product chains. Robust and compact. Best for understanding reaction sequences.

  • 'grid': 2D spatial layout using KGML coordinates. Shows the pathway topology with box-and-arrow rendering. Best for seeing spatial relationships.

Args: pathway_id: KEGG pathway ID (e.g. 'hsa00010' for human glycolysis). Must be organism-specific; reference pathways (map*) have limited KGML. style: 'chain' (default, linear text) or 'grid' (2D spatial layout). max_width: Maximum line width in characters (40-200, default 100). max_height: Grid mode only: maximum height in lines (20-80, default 40).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
styleNochain
max_widthNo
max_heightNo
pathway_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations already indicate readOnly, idempotent, and openWorld hints. The description adds behavioral details: ASCII output, style options, max dimensions, and the KGML limitation. It does not disclose error handling or async behavior, but the annotations cover the key traits.

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

Conciseness5/5

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

Concise and well-structured: one-line overview, clear bullet-like explanation of styles, and parameter list with all necessary details. No redundant sentences.

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?

Given the output schema exists (not shown), the description does not need to detail return values. It covers all relevant aspects: pathway ID requirements, style choices, and layout constraints. Complete for a simple rendering tool.

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

Parameters5/5

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

Schema description coverage is 0%, so the description fully explains each parameter. Pathway_id includes an example and constraint; style explains the two options with recommendations; max_width and max_height have ranges and defaults. All parameters are well-documented.

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?

The description clearly states 'Render a KEGG pathway as ASCII text optimized for LLM consumption.' It differentiates from sibling tools (e.g., search_pathways, get_pathway_info) which do not render paths. The two styles are explicitly named and their purposes are defined.

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

Usage Guidelines5/5

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

Provides explicit guidance: style 'chain' for reaction sequences, 'grid' for spatial relationships. Also notes that pathway_id must be organism-specific and reference pathways have limited KGML, which helps the agent choose correctly.

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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