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berntpopp
by berntpopp

Get Protein Variants

get_protein_variants
Read-onlyIdempotent

Retrieve natural protein variant annotations from UniProt, including position, substitution, HGVS notation, disease associations, and dbSNP IDs. Optionally filter to disease-linked variants only.

Instructions

Return natural-variant annotations for an entry: position, wild-type residue, amino-acid substitution, an HGVS-style notation (e.g. L176F) for simple substitutions, variant_type (substitution|other), free-text description, structured linked diseases, and dbsnp rsIDs. Set disease_associated_only=true to keep only disease-linked variants. Signature: get_protein_variants(accession, limit=, disease_associated_only=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYesUniProtKB accession, e.g. P05067 (isoforms like P05067-2 accepted).
limitNoMax variants to return.
disease_associated_onlyNoReturn only variants linked to a disease.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
accessionNo
countNo
variantsNo
truncatedNo
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true. The description adds behavioral context by listing return fields and providing an example notation format. No contradictions; adds detail 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 concise (two sentences plus signature), front-loaded with purpose, and every sentence adds value. No unnecessary words or repetition. Efficiently communicates key information.

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 has 3 parameters, full schema coverage, and an output schema, the description is complete enough. It explains return fields, filter usage, and signature. Could mention pagination or rate limits, but not essential. Overall very good coverage.

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?

Schema coverage is 100% with good descriptions. The description adds a signature line showing function call format and explains the effect of disease_associated_only. Also provides an example of the notation field. Adds value beyond schema.

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 returns 'natural-variant annotations for an entry' and lists specific fields (position, wild-type residue, substitution, notation, variant_type, description, diseases, dbsnp). This distinguishes it from sibling tools like get_protein_features or get_protein_diseases by focusing on variants.

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 a specific usage example: 'Set disease_associated_only=true to keep only disease-linked variants.' It does not explicitly contrast with sibling tools, but the context and parameter description imply when to use the filter. Lacks explicit when-not-to-use guidance.

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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