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geo_get

Retrieve complete GEO SOFT records for series, samples, or platforms, including summaries, organisms, supplementary files, and cross-references. Optionally download the first supplementary file.

Instructions

Get the full SOFT record details for a GEO entry: series (GSE...), sample (GSM...), or platform (GPL...).

A series detail includes summary, organisms, platform_ids, a sample preview, supplementary file URLs, and cross-references for chaining: sra → sra_get(SRP.../SRR...), pubmed_ids → article_get, samples → geo_get(GSM...), platform_ids → geo_get(GPL...).

download=true additionally saves the first supplementary file (.gz/.csv/.txt, subject to max_bytes) to a local temp path and returns its path, size, and source URL.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
downloadNoDownload the first supplementary file (.gz) to a local temp path
accessionYesGEO accession (GSE series, GSM sample, or GPL platform; GDS curated DataSets return guidance pointing at the underlying GSE/GSM)
max_bytesNoSize cap in bytes for the downloaded supplementary file (default 52428800 = 50 MB)
Install Server

TDQS

A4.2/5.0
Behavior4/5

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

The description discloses the main non-read-only behavior outside the annotations: download=true saves the first supplementary file to a local temp path and returns path/size/source URL, capped by max_bytes. This goes beyond readOnlyHint=false and openWorldHint=true, and it is consistent with them.

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 organized with a front-loaded core purpose, a compact enumeration of series-level return fields, and a separate sentence for the opt-in download behavior. Every sentence contributes either scope, chaining context, or side-effect disclosure, with no filler.

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 no output schema, the description adequately covers return contents for series lookups and the download path, and it explains the tool's role in chaining across siblings. It is slightly less complete for sample/platform return shapes, but the 'full SOFT record details' framing plus the series example gives sufficient context for an agent to invoke it correctly.

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?

The schema already fully describes all three parameters, so this is at baseline 3. The description adds value by clarifying accepted accession patterns, download file extensions (.gz/.csv/.txt), and the non-boolean effect of download, which strengthens the parameter story.

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 and resource: 'Get the full SOFT record details for a GEO entry', and enumerates the accession types (GSE/GSM/GPL). It clearly distinguishes this lookup tool from search-oriented siblings like geo_search by emphasizing full record details and chaining cross-references.

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?

Usage context is implied rather than explicit: the description explains what series/sample/platform lookups return and shows chaining paths (sra_get, article_get, geo_get), but it never states when to prefer geo_get over geo_search, batch_get, or other GET tools. A clear when-to-use statement 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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