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bioretrieval-mcp

bioretrieval-mcp

by axle962
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

Search GEO methylation series

search_geo_methylation
Read-onlyIdempotent

Search NCBI GEO for DNA-methylation series by free-text query and Illumina array platform, returning matching GSE accessions, titles, sample counts, organisms, and PubMed links.

Instructions

Search NCBI GEO for DNA-methylation series (GSE) run on a given Illumina array.

Returns total hit count plus, per series: accession, title, summary (truncated), platforms, sample count, organisms, submission date and linked PubMed IDs.

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": {
      "query": "<query>",
      "platform": "<platform>"
    },
    "name": "search_geo_methylation"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNoMaximum series to return.
queryYesFree-text GEO query, e.g. 'Alzheimer brain', 'aging blood', 'colorectal cancer'.
platformYesIllumina array: 27K (GPL8490), 450K (GPL13534), EPIC (GPL21145), EPICv2 (GPL33022).

Output Schema

NameRequiredDescriptionDefault
queryYes
seriesYes
platformYes
returnedYes
total_countYesTotal matching series in GEO (results are paged)
platform_gplsYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent and openWorld, so the safety profile is covered. The description adds genuine behavioral detail beyond that: it returns a total hit count and flags that summaries are truncated — a real caveat an agent should know when consuming results.

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?

Two sentences, zero waste. The action and scope come first, followed by the return payload, which is the correct front-loading for a search tool.

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?

With an output schema present and full parameter documentation, the description only needs to frame scope and caveats, which it does. Minor gaps remain: no mention of result ordering or whether 'limit' paginates or merely truncates the hit set.

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%, so all three parameters (limit, query, platform with GPL mappings) are already documented in the schema. The description only restates the 'given Illumina array' constraint and adds no syntax, default, or result-ordering detail beyond the schema.

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+resource ('Search NCBI GEO for DNA-methylation series (GSE)') plus a scoping constraint ('run on a given Illumina array'). Sibling tools (search_emdb, get_uniprot) are in entirely different domains, so no confusion is possible.

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 domain context ('DNA-methylation series on an Illumina array') implies appropriate usage, but there is no explicit when-to-use guidance, no exclusions, and no mention of alternatives for e.g. non-methylation or non-array GEO records.

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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