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Glama

geo_get

Retrieve full GEO series, sample, or platform records by accession, including metadata, cross-references, and supplementary file URLs; optionally download a supplementary file to a temp path.

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...).

GDS accessions (curated DataSets, not served by SOFT) return structured guidance as data — { accession, guidance, see_also: { series: "GSE…", sample: "GSM…" } } — pointing at the underlying series/sample records; this is a successful result, not an error. Malformed accessions still fail at schema validation.

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

Input Schema

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

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
    • addedInput schema / properties / max_bytes / maximum
      Added value: +9007199254740991
  2. Changed2 schema fields changedv1.6.0-alpha.7
    • changedInput schema / properties / accession / description
      Previous value: -"GEO accession (GSE series, GSM sample, or GPL platform; GDS curated DataSets return guidance pointing at the underlying GSE/GSM)"New value: +"GEO accession (GSE series, GSM sample, or GPL platform; GDS curated DataSets return structured guidance pointing at the underlying GSE/GSM)"
    • changedInput schema / properties / download / description
      Previous value: -"Download the first supplementary file (.gz) to a local temp path"New value: +"Download a supplementary file to a local temp path (prefers .gz/.csv/.txt, else the first listed)"
  3. Addedv0.7.1

TDQS

A4.3/5.0
Behavior5/5

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

Annotations declare readOnlyHint=false and openWorldHint=true; the description explains why a 'get' is not read-only — download=true writes a supplementary file to a local temp path and returns path/size/source URL. It also discloses the non-obvious GDS behavior (structured guidance returned as a successful result, not an error) and that malformed accessions fail schema validation, which is exactly the context an agent needs to interpret results.

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

Conciseness4/5

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

Front-loaded with the core purpose in the first sentence, then chaining, then edge cases in descending priority — good ordering. The download paragraph duplicates the schema's file-preference wording and could be trimmed to a pointer.

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 must describe returns and does so for series (summary, organisms, platform_ids, sample preview, supplementary URLs, cross-references), for GDS, and for download. Return shapes for GSM sample and GPL platform records are left unspecified, a minor but real gap.

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 description coverage is 100%, and the schema already documents the .gz/.csv/.txt preference and the max_bytes default, so the description largely restates structured data. It adds the 'subject to max_bytes' linkage between download and the size cap, but nothing beyond that; baseline 3 is appropriate when the schema carries the weight.

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 and resource ('Get the full SOFT record details for a GEO entry') and immediately enumerates the three accession families (GSE/GSM/GPL), which cleanly separates it from the geo_search sibling. An agent knows this is the record-fetch step, not the discovery step.

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?

Explicitly maps returned cross-references to the follow-up tools (sra → sra_get, pubmed_ids → article_get, samples → geo_get(GSM...), platform_ids → geo_get(GPL...)), giving strong chaining context, and explains what happens with GDS accessions. It does not state the inverse condition (use geo_search first to obtain an accession), so the routing is clear but not fully bidirectional.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.