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uniprot_get_publications

Read-only

Retrieve publications citing a UniProt entry, including PubMed IDs, DOIs, titles, authors, journal, year, and the specific experimental work each citation supports (e.g., CRYSTALLIZATION, PHOSPHORYLATION).

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
accessionYesUniProt accession, e.g. 'P04637' (human TP53) or 'P38398' (human BRCA1). Both reviewed (Swiss-Prot) and unreviewed (TrEMBL) accessions are accepted; case-sensitive.
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 that the tool is a pure composition with no additional HTTP calls, and lists the specific fields returned (e.g., reference position annotations). This provides useful behavioral 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.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, front-loaded paragraph that efficiently conveys all necessary information without extraneous words.

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?

With an output schema present, the return values are already documented. The description covers the key content (fields, reference position examples), making it complete for a list operation.

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

Parameters3/5

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

Schema coverage is 100%, so the schema already documents both parameters. The description adds minimal extra detail beyond restating the schema's description. Baseline 3 is appropriate.

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 it lists publications UniProt cites on an entry, with specific fields like PubMed IDs, DOIs, titles, authors, etc. It distinguishes from siblings by being a direct retrieval for a given entry, not a search or other operation.

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 implies usage by stating it's a composition over the entry's references block with no extra HTTP call, suggesting efficiency. However, it does not explicitly state when to use vs alternatives or provide exclusions.

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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