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Summarize Collection

encode_summarize_collection
Read-onlyIdempotent

Get a bird's-eye view of your tracked experiments grouped by assay, target, and organ. Summarizes counts of publications, derived files, and references to reveal collection gaps.

Instructions

Summarize your tracked experiment collection with grouped statistics.

Provides an overview of tracked experiments grouped by assay type, target, organism, organ, biosample type, and lab. Shows total counts for publications, derived files, and external references.

Useful when tracking 10+ experiments and needing a bird's-eye view of your research data collection.

WHEN TO USE: Use for a bird's-eye view of tracked experiments grouped by assay, target, organ. Best for 10+ tracked experiments. RELATED TOOLS: encode_list_tracked, encode_export_data

Args: assay_title: Filter by assay type (partial match) organism: Filter by organism (partial match) organ: Filter by organ (partial match)

Returns: JSON summary with experiment counts grouped by multiple dimensions.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
assay_titleNo
organismNo
organNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so the description doesn't need to repeat that. It adds value by noting partial match parameter behavior, but no extra details on auth or rate limits. Still, it goes beyond annotations.

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?

Well-structured with clear sections (description, when to use, related tools, args). The phrase 'bird's-eye view' appears twice, slightly redundant, but overall concise and informative.

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

Completeness5/5

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

Given an output schema exists, the description appropriately summarizes return type (JSON summary). Covers parameters, usage context, and grouping dimensions. No gaps for a summarization tool.

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?

With 0% schema coverage, the description compensates by explaining each parameter's purpose (filter by assay, organism, organ) and noting partial match behavior. Lacks format details but provides essential context.

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 tool summarizes tracked experiments with grouped statistics, specifying grouping dimensions (assay, target, organism, etc.) and distinguishing it from siblings like encode_list_tracked and encode_export_data.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicit WHEN TO USE guidance is provided: 'best for 10+ tracked experiments' and 'bird's-eye view.' Also lists related tools (encode_list_tracked, encode_export_data) to help differentiate.

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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