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Get Citations

encode_get_citations
Read-onlyIdempotent

Retrieve publications and citations for ENCODE experiments. Export data in JSON, BibTeX, or RIS format for reference managers.

Instructions

Get publications and citations for tracked experiments.

Returns publication data with authors, journal, DOI, PMID. Can export as BibTeX or RIS (Endnote/Zotero/Mendeley compatible).

WHEN TO USE: Use to get publication data for tracked experiments. Supports BibTeX and RIS export for reference managers. RELATED TOOLS: encode_track_experiment, encode_link_reference

Args: accession: Specific experiment accession. If None, returns all publications. export_format: Output format: - "json": Structured data (default) - "bibtex": BibTeX format for LaTeX - "ris": RIS format (Endnote, Zotero, Mendeley)

Returns: Publications in the requested format.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionNo
export_formatNojson

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

Annotations already declare readOnly, not destructive, and idempotent. The description adds context about return structure and export capabilities but does not disclose additional behavioral traits beyond the annotations. No contradictions.

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 sections for purpose, usage, args, and returns. Moderately concise; every sentence adds value. Could be slightly tighter but effective overall.

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?

Given the tool's simplicity (2 optional parameters) and the presence of an output schema, the description provides sufficient context: lists return fields, export options, and a usage section. No major gaps.

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?

Despite 0% schema description coverage, the description's 'Args' section explains both parameters in detail, including the meaning of accession and the available export_format enum values. This compensates fully for the lack of schema descriptions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool gets publications and citations for tracked experiments, listing returned fields (authors, journal, DOI, PMID) and export formats. However, it does not explicitly differentiate from a potentially similar sibling tool 'encode_get_references', which may serve a similar purpose.

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?

Includes a dedicated 'WHEN TO USE' section and mentions related tools. Provides guidance on export formats for reference managers. Lacks explicit exclusions or alternatives for when this tool should not be used.

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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