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Export Tracked Data

encode_export_data
Read-onlyIdempotent

Export tracked ENCODE experiments as a CSV, TSV, or JSON table with metadata, publication counts, and PMIDs. Ideal for manuscripts, reports, and further literature analysis.

Instructions

Export tracked experiments as a table (CSV, TSV, or JSON).

Creates a tabular export of all tracked experiments with metadata, publication counts, PMIDs, and derived file counts. Useful for loading into Excel, R, pandas, or sharing with collaborators.

PMIDs in the output can be directly used with PubMed MCP tools for further literature analysis.

WHEN TO USE: Use to create shareable tables of tracked experiments (CSV, TSV, JSON). Good for manuscripts and reports. RELATED TOOLS: encode_list_tracked, encode_summarize_collection

Args: format: Output format: - "csv": Comma-separated values (default, for Excel/spreadsheets) - "tsv": Tab-separated values (for R, pandas) - "json": JSON array (for programmatic use) assay_title: Filter by assay type (partial match) organism: Filter by organism (partial match) organ: Filter by organ (partial match)

Returns: Formatted table data in the requested format.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
formatNocsv
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 mark the tool as read-only, non-destructive, and idempotent. The description adds that the output includes specific fields, filters support partial matching, and that generated PMIDs are usable with PubMed MCP tools. However, it does not disclose potential export limits or pagination behavior.

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 well-structured with sections for purpose, content details, usage context, related tools, parameters, and returns. Every sentence serves a purpose, and the most important information (what it exports and format options) appears first.

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 has an output schema, the description adequately explains what the tool does, its parameters, and how results can be used. It covers filtering, format variants, and integration with other tools, making it sufficiently complete for an agent to understand and invoke 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 provides 4 parameters with no descriptions (0% coverage). The description compensates by explaining format options with use cases (csv for Excel, tsv for R/pandas, json for programmatic use) and clarifying that filter parameters use partial matching. This adds meaningful context beyond the raw schema.

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 'Export tracked experiments as a table (CSV, TSV, or JSON)' and lists included metadata, publication counts, PMIDs, and derived file counts. It distinguishes from related tools like encode_list_tracked and encode_summarize_collection.

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?

The description includes a 'WHEN TO USE' section ('Use to create shareable tables... for manuscripts and reports') and lists related tools. It explains the output's utility with PubMed MCP tools, but does not explicitly state when not to use or provide alternative selection criteria.

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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