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Summarize Collection

encode_summarize_collection
Read-onlyIdempotent

Generate statistical summaries of tracked ENCODE experiments grouped by assay, target, organism, and biosample to provide research collection overviews.

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 cover read-only, non-destructive, and idempotent behavior, but the description adds valuable context: it specifies the tool is 'useful when tracking 10+ experiments' and describes the output format ('grouped by multiple dimensions'). 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?

Well-structured with clear sections (description, usage, related tools, args, returns). Every sentence adds value: the first explains the core function, the second specifies use cases, and the rest provide practical guidance without redundancy.

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 the tool's moderate complexity, rich annotations (readOnlyHint, idempotentHint), and presence of an output schema, the description is complete. It covers purpose, usage context, parameters, and return format, leaving no significant gaps for agent understanding.

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 0%, so the description must compensate. It explains that parameters are filters with 'partial match' behavior, adding meaning beyond the schema's basic titles. However, it doesn't detail all three parameters individually or provide examples.

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's purpose with specific verbs ('summarize', 'provides an overview') and resources ('tracked experiment collection'). It distinguishes from siblings by specifying it's for grouped statistics and overviews, unlike list_tracked (listing) or export_data (exporting).

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 guidance is provided: 'WHEN TO USE' section states it's for a bird's-eye view with 10+ experiments, and 'RELATED TOOLS' names encode_list_tracked and encode_export_data as alternatives. This clearly indicates when to use this tool versus others.

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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