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uniprot_search_citations

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Search UniProt citations by title, author, or year to find citation IDs like PubMed IDs. Supports free text and field-specific queries for targeted results.

Instructions

Search the UniProt citations index (the literature UniProt references) by title, author, or year. Use this to find a citation's ID (typically a PubMed ID); once you have it, call uniprot_get_citation for the full record. For the publications attached to one specific protein entry, use uniprot_get_publications instead. Returns up to size matches, or an empty list if nothing matches. Examples: 'p53 AND author:Vogelstein', 'BRCA1 AND year:[2020 TO 2024]'.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sizeNoMaximum number of results to return; capped at 500 server-side.
queryYesCitation query using UniProt citation fields, e.g. 'p53 AND author:Vogelstein' or 'BRCA1 AND year:[2020 TO 2024]'. Supports free text plus 'author:', 'title:', and 'year:' ranges.
response_formatNo'markdown' (default) for a human-readable report with a provenance footer, or 'json' for a machine-parseable structured payload with the same data. Any other value is rejected.markdown

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=true and openWorldHint=true. The description adds return behavior (up to size matches, empty list if none) and a server-side cap of 500, which provides useful context beyond the annotations but does not discuss side effects or auth requirements.

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 concise, front-loaded with purpose, and every sentence adds value (purpose, workflow, sibling differentiation, examples, behavior). No wasteful text.

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 output schema exists (context signal), the description adequately covers tool behavior, parameter usage, and differentiation among many sibling tools. It provides sufficient context for an agent to select and invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, baseline 3. The description significantly enhances meaning: explains query syntax with fields like author:, title:, year: ranges, gives examples, clarifies size cap, and describes response_format options including that invalid values are rejected.

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 searches the UniProt citations index by title, author, or year, and explicitly distinguishes from sibling tools like uniprot_get_citation and uniprot_get_publications.

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?

It explains the workflow: find a citation's ID with this tool, then call uniprot_get_citation for full record. It also provides an alternative for protein-specific publications (uniprot_get_publications) and includes query examples.

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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