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geo_search

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Search NCBI GEO for functional genomics studies, including expression microarrays and RNA-seq. Query by free text or accession to retrieve results linked to related data.

Instructions

Search NCBI GEO (Gene Expression Omnibus) for functional genomics studies — expression microarrays, RNA-seq, and other high-throughput sequencing series.

Queries accept plain terms ("breast cancer RNA-seq", "melanoma single cell") or NCBI field syntax ("GSE183947[Accession]"). Each result carries cross-links for chaining: sra_project → sra_get, bioproject, pubmed_ids → article_get, and accession → geo_get for full details.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum results
queryYesFree-text GEO search terms, e.g. "breast cancer RNA-seq", "melanoma single cell"
offsetNoResult offset for pagination
organismNoFilter by organism (e.g. "Homo sapiens", "Mus musculus")
entry_typeNoGEO entry type — gse=study (default), gsm=sample, gpl=platform, gds=curated dataset
Install Server

TDQS

A4.4/5.0
Behavior4/5

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

With readOnlyHint and openWorldHint annotations already covering safety and non-exhaustiveness, the description adds useful behavioral detail: accepted query syntax (plain terms vs NCBI field syntax) and that each result carries cross-links for chaining to sra_get, article_get, and geo_get. No contradiction with annotations.

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?

Three compact sentences convey purpose, query syntax, and result chaining. The description is front-loaded with the core action and contains no filler or redundant restatement of the schema.

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 search tool with no output schema, the description covers scope, accepted query forms, and result linkage, while the input schema fully documents all parameters. It could go one step further by describing the shape of individual search results, but the cross-link details and schema coverage make it complete enough for correct invocation.

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

Parameters4/5

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

Schema description coverage is 100%, so the baseline is 3. The description adds extra semantics for the query parameter by showing that it accepts both plain language and structured NCBI fields, with concrete examples like 'GSE183947[Accession]'.

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 opens with a specific verb-resource-object construction: 'Search NCBI GEO ... for functional genomics studies'. It lists concrete content types and query examples, and differentiates itself from geo_get by noting 'accession → geo_get for full details'.

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 description gives clear context: use this tool to search GEO by terms or NCBI field syntax, then chain to related tools via cross-links. It names geo_get as the follow-up for full details, but does not explicitly exclude overlapping search siblings such as sra_search or genbank_search.

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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