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get_string_ids

Map protein names, synonyms, and UniProt IDs to STRING identifiers for protein-protein interaction analysis using NCBI taxon IDs to specify species.

Instructions

Map protein names, synonyms, and UniProt identifiers to STRING identifiers. Species parameter uses NCBI taxon IDs (e.g., 9606 for human, 10090 for mouse).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifiersYesProtein names or IDs, newline or space-separated (e.g., 'TP53 BRCA1' or 'P04637')
speciesNoNCBI taxon ID (e.g., 9606 for human, 10090 for mouse)
limitNoMaximum number of STRING identifiers to return per query protein
echo_queryNoInclude the submitted identifier in the output
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions the mapping function and species parameter format but fails to describe key behaviors like error handling, rate limits, authentication needs, or what happens with ambiguous matches, leaving significant gaps for a tool with 4 parameters.

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 in the first sentence and uses a second sentence to clarify the species parameter, with no wasted words. Every sentence adds necessary context efficiently.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's moderate complexity (4 parameters, no output schema, no annotations), the description is adequate for basic use but incomplete. It covers the mapping purpose and species format but lacks details on output format, error cases, or behavioral constraints, which are crucial for effective agent invocation.

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 description coverage is 100%, so the schema already documents all parameters thoroughly. The description adds minimal value by reiterating the species parameter format (e.g., 9606 for human) and implying identifier types, but doesn't provide additional syntax or format details beyond what the schema offers, meeting the baseline for high coverage.

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's purpose with specific verbs ('Map') and resources ('protein names, synonyms, and UniProt identifiers to STRING identifiers'), distinguishing it from siblings like 'get_enrichment' or 'get_network' by focusing on identifier mapping rather than enrichment or network analysis.

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 by specifying input types (protein names, synonyms, UniProt IDs) and the species parameter, but lacks explicit guidance on when to use this tool versus alternatives like 'resolve_proteins' or other siblings, leaving the agent to infer context from tool names alone.

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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