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uniprot_get_publications

Read-only

Retrieve publications cited by UniProt for a protein entry, including PubMed IDs, DOIs, titles, authors, and experimental annotations like crystallography or phosphorylation sites.

Instructions

List the publications UniProt cites on an entry, with PubMed IDs, DOIs, titles, authors, journal, year, and the 'reference position' annotation (the experimental work each citation supports — e.g. 'CRYSTALLIZATION', 'PHOSPHORYLATION AT SER-15', 'INVOLVEMENT IN LI-FRAUMENI SYNDROME'). Pure composition over the entry's references block — no extra HTTP call beyond the entry fetch.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYes
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations already indicate readOnlyHint=true and openWorldHint=true. The description adds that the operation is pure composition without extra HTTP calls, which surfaces behavioral efficiency. It also lists the exact fields returned, providing additional context 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?

The description is a single, well-structured sentence that front-loads the purpose and includes important details (fields, composition nature). It is slightly long but every part adds value, so it remains concise.

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 simple purpose and presence of output schema, the description covers what is fetched. It could mention that it requires a valid UniProt accession, but that is implicit. The behavioral efficiency note adds completeness, and the sibling list provides context for selection.

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

Parameters2/5

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

The input schema has two parameters, but the description does not explain them. With 0% schema description coverage, the description should compensate, but it fails to describe what 'accession' or 'response_format' mean. Although the names are somewhat self-explanatory, the description could add value by specifying valid formats or 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 lists publications cited by UniProt for an entry, including specific fields like PubMed IDs, titles, and reference positions. It distinguishes itself from siblings by noting it is a pure composition over the entry's references block.

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 explicitly says when to use: to list publications on an entry. It mentions the lightweight nature (no extra HTTP call), implying it is appropriate for quick access. However, it does not explicitly state when not to use or list alternatives, though sibling tool names provide context.

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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