propaths-mcp

export_network

Read-onlyIdempotent

Export a protein's interactome as a directed edge list in TSV, SIF, or GraphML format for use in Cytoscape, networkx, igraph, or Gephi.

Instructions

Export a protein's interactome as text for external tools.

format = tsv (edge list / spreadsheet), sif or graphml (Cytoscape, networkx, igraph, Gephi). Edges carry their biological orientation (an upstream partner points into the protein), so the graph is directed.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "symbol": "<symbol>"
    },
    "name": "export_network"
  }
}

Input Schema

Name	Required	Description	Default
`format`	No		tsv
`symbol`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.1Aug 27, 2026

TDQS

A3.8/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and idempotentHint=true, so the description's burden is lower. It adds useful context: edges carry biological orientation and the graph is directed. However, it does not disclose other behavioral traits like error handling, data volume, or response structure beyond the output schema.

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?

The description is two concise sentences that front-load the main purpose and immediately provide essential format details and a behavioral note (directedness). No redundancy or fluff exists.

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

Completeness4/5

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

For a simple 2-parameter tool with an output schema and safety-oriented annotations, the description is largely complete. It could explicitly state that 'symbol' is a protein identifier, but this is heavily implied by 'a protein's interactome'.

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 0%, so the description must compensate. It explains the 'format' parameter's allowed values (tsv, sif, graphml) and their typical use cases, but it does not describe the 'symbol' parameter beyond the implied protein context, leaving it under-specified.

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 a specific verb ('Export'), resource ('a protein's interactome'), and purpose ('for external tools'). It also lists concrete output formats (tsv, sif, graphml) and notes directedness, distinguishing it from sibling tools like get_interaction or list_interactions that retrieve data directly.

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

Usage Guidelines3/5

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

The description implies this tool is for exporting interactome data for external analysis, but it does not explicitly state when to prefer it over alternatives, nor does it mention when not to use it. The context (format options and directedness) partially informs usage, but explicit routing is missing.

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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