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io.github.rcsb/rcsb-mcp

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rcsb_get_uniprot

Read-onlyIdempotent

Retrieve UniProt functional summaries, protein names, organism, and keywords for a given accession. Optionally expand fields to fetch GO terms, domains, features, and external references.

Instructions

Fetch the UniProt record RCSB maps to an accession, e.g. "P69905".

Default fields give a functional snapshot: accession(s), entry name, protein and gene names, EC number, the UniProt function comment, source organism, and keywords (which often summarize biology directly, e.g. "ATP-binding", "Viral attachment to host entry receptor").

RCSB's UniProt integration is rich — fields can also pull the heavier annotation sets (kept out of the default because they can run to hundreds of entries): rcsb_uniprot_annotation (GO terms, InterPro, disease associations), rcsb_uniprot_feature (domains, sites, binding sites, sequence variants), and rcsb_uniprot_external_reference.

Args: uniprot_id: a UniProt accession, e.g. "P69905". fields: Optional GraphQL selection replacing the curated default (e.g. "rcsb_uniprot_protein.name"); discover/verify paths with rcsb_describe_data_object("uniprot") (see the server instructions).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fieldsNo
uniprot_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

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

Even with readOnlyHint, openWorldHint, and idempotentHint already declared, the description adds meaningful behavioral detail: default fields are curated for a functional snapshot, heavier annotation sets can run to hundreds of entries and are deliberately kept out of defaults, and the `fields` parameter replaces the curated default. This goes well beyond what annotations alone convey.

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 front-loaded with the core purpose, then organized into default vs. optional field behavior, then a clear Args block. Every sentence adds value—no filler or repetition of schema/annotations.

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 is a single-record fetch with a relatively rich output schema, the description covers the important context: default fields, optional heavy annotations, and how to verify custom field paths. It even references server instructions for deeper context, making the tool self-sufficient for an agent.

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 0%, so the description carries full responsibility for parameter meaning. It explains `uniprot_id` as a UniProt accession with an example, and `fields` as an optional GraphQL selection with examples and a discovery path (`rcsb_describe_data_object("uniprot")`). This fully compensates for the schema's lack of descriptions.

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 opens with a specific verb+resource: 'Fetch the UniProt record RCSB maps to an accession', which clearly distinguishes this from the many search- and entry-focused sibling tools. The example accession P69905 adds immediate concreteness.

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 gives strong contextual guidance: it explains the default functional snapshot and when to opt into heavier annotation sets via the `fields` parameter. It does not explicitly name alternatives or when-not-to-use this tool, but the unique resource and clear access path make the intended usage unambiguous.

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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