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berntpopp
by berntpopp

Find Proteins (Batch)

find_proteins_batch
Read-onlyIdempotent

Resolve multiple gene symbols to UniProtKB entries concurrently. Returns per-gene accessions, protein lists, and identifies unmatched genes. Ideal for multi-gene protein lookups.

Instructions

Resolve SEVERAL gene symbols to UniProtKB entries in ONE call, running the lookups concurrently -- so N genes cost about one cold round-trip instead of N sequential ones. Use this for multi-gene tasks (e.g. 'get domains for PNKP and NAA10'). Returns by_gene (gene -> accessions, reviewed-first), a flat proteins list tagged with matched_gene, resolved_genes, and unresolved_genes (a symbol that matched nothing is disclosed, never silently dropped). Optionally scope by organism_taxon and reviewed. next_commands fan out to get_protein on each resolved gene's top hit. For a single gene use find_proteins. Signature: find_proteins_batch(genes, organism_taxon=, reviewed=, limit_per_gene=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
genesYesGene symbols to resolve, e.g. ['PNKP','NAA10'].
organism_taxonNoNCBI taxon id, e.g. 9606 for human.
reviewedNoTrue = Swiss-Prot only; False = TrEMBL only.
limit_per_geneNoMax entries per gene (default 5).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
gene_countNo
countNo
by_geneNo
proteinsNo
resolved_genesNo
unresolved_genesNo
Behavior5/5

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

Annotations already declare readOnly, idempotent, non-destructive. Description adds significant behavioral details: concurrent lookups, return structure (by_gene with matched_gene, resolved_genes, unresolved_genes), and that unresolved symbols are disclosed, never silently dropped. No contradiction 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.

Conciseness5/5

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

Description is concisely structured: front-loaded with purpose and concurrency benefit, then usage example, return details, optional scoping, and sibling differentiation. Every sentence earns its place with no fluff.

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 4 parameters, rich annotations, and an output schema, the description is fully complete. It covers purpose, usage, behavioral details, parameter context, return structure, and next steps. No gaps identified.

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 100%, but the description adds substantial meaning beyond it: explains concurrency benefit, clarifies return structure, and provides a signature line. Parameter descriptions in schema are clear, but description contextualizes them (e.g., limit_per_gene default and max).

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 resolves several gene symbols to UniProtKB entries in one call, using strong verb-resource 'Resolve SEVERAL gene symbols to UniProtKB entries' and explicitly distinguishes from sibling 'find_proteins' by noting batch vs single gene usage.

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

Usage Guidelines5/5

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

The description gives explicit usage guidelines: use for multi-gene tasks (e.g., 'get domains for PNKP and NAA10'), states that for a single gene use find_proteins, and provides next_commands direction (fan out to get_protein).

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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