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berntpopp
by berntpopp

Get Protein

get_protein
Read-onlyIdempotent

Retrieve core summary for a UniProtKB entry by accession, including protein details, function, and presence flags for variants, diseases, and structures.

Instructions

Return the core summary for a single UniProtKB entry by accession: mnemonic, reviewed flag, recommended/short name, gene(s), organism + taxon, protein existence, sequence length and mass, a function summary, and creation/modification dates, plus has_variants/has_diseases/has_structure presence flags that drive content-aware next_commands. An obsolete/demerged accession returns a flagged obsolete record (obsolete:true + replaced_by). response_mode (default compact) controls verbosity; standard/full add the created/modified dates. Signature: get_protein(accession, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYesUniProtKB accession, e.g. P05067 (isoforms like P05067-2 accepted).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
accessionNo
requested_accessionNo
mnemonicNo
reviewedNo
recommended_nameNo
genesNo
organismNo
taxon_idNo
sequence_lengthNo
mass_daNo
obsoleteNo
replaced_byNo
has_variantsNo
has_diseasesNo
has_structureNo
isoformNo
Behavior5/5

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

The description goes beyond annotations by explaining behavior for obsolete/demerged accessions (obsolete flag and replaced_by field) and detailing the response_mode parameter's effect on verbosity and included dates. No contradictions with 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, dense sentence that efficiently conveys all necessary information. It could be slightly more structured, but it remains concise and front-loaded.

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's complexity (two parameters, output schema, rich annotations), the description is highly complete. It covers edge cases (obsolete accessions), response modes, and flags for guiding next steps.

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?

Although the schema has 100% coverage, the description adds context by providing an example accession, explaining the response_mode enum values (minimal, compact, standard, full) and their impact on output.

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 that the tool returns the core summary for a single UniProtKB entry by accession, listing specific fields. It distinguishes from sibling tools that focus on specific aspects (e.g., get_protein_sequence, get_protein_variants).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for retrieving core summary data and mentions flags that drive next commands, but it does not explicitly state when to use this tool versus alternatives or when not to use it.

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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