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search_datasets

Search multiple public life-science data repositories at once and retrieve ranked datasets matching your query, with optional filters for organism, data type, and open access.

Instructions

Search all registered open data sources at once and return ranked datasets.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
textYesWhat the data should contain, e.g. "lung adenocarcinoma scRNA-seq".
sourcesNoRestrict to these sources (see list_sources). Default: all.
organismNoScientific or common name, e.g. 'Homo sapiens' or 'mouse'.
data_typesNoOnly query sources covering any of these data types.
min_samplesNoDrop records with fewer samples. Records whose sample count is unknown (many sources do not report it) are kept.
expand_ontologyNoAlso search ontology synonyms of the text (EBI OLS).
limit_per_sourceNoMaximum records fetched from each source.
open_access_onlyNoDrop records marked controlled-access. Unknown access is kept.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
errorsNo
resultsYes
sources_queriedNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

B3.4/5.0
Behavior2/5

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

With no annotations provided, the description must disclose behavioral traits. It mentions the ranked output, which adds value, but it does not state that the operation is read-only, any potential side effects, access restrictions, or rate limits. For a search tool this is a notable gap; the 'search' verb only implicitly suggests safety.

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 a single concise sentence that front-loads the primary purpose and output. There is no filler or redundancy; every word contributes to understanding the tool's core function.

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

Completeness2/5

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

The description is minimal for a tool with 8 parameters and an output schema. It does not explain the ranking mechanism, the significance of the open-access qualifier, or how parameters like expand_ontology or min_samples affect results. While the output schema covers return values, the description fails to tie the high-level behavior to the many available options, leaving an agent without sufficient context for nuanced use cases.

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% with detailed descriptions for all 8 parameters, so the baseline is 3. The tool description adds no parameter-specific information beyond what the schema already provides, leaving the parameters fully explained by the schema alone.

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 the action (search), the resource (all registered open data sources), and the output (ranked datasets). It distinguishes itself from siblings like get_dataset (which retrieves a specific dataset) and list_sources (which lists sources) by emphasizing the cross-source, aggregated search scope.

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 usage when a broad cross-source search is needed, but it does not explicitly mention when to use alternatives (get_dataset for a known dataset, list_sources to discover sources). No exclusions or conditional guidance is provided, so the agent must infer the appropriate context.

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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