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get_network

Retrieve protein-protein interaction networks with confidence scores to analyze relationships between specified proteins. Supports functional or physical network types with customizable scoring thresholds.

Instructions

Retrieve protein-protein interaction network for given proteins. Returns network edges with confidence scores.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
identifiersYesProtein names or STRING IDs, newline or space-separated
speciesNoNCBI taxon ID
required_scoreNoMinimum interaction confidence score (0-1000)
network_typeNoType of network (functional includes all evidence, physical only direct interactions)functional
add_nodesNoNumber of additional nodes to add to the network
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It mentions the return format but doesn't cover important aspects like whether this is a read-only operation (implied by 'retrieve'), potential rate limits, authentication requirements, error conditions, or how large networks are handled. The description is minimal and lacks behavioral context.

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 extremely concise - just two sentences that directly state the tool's purpose and return format. Every word earns its place with zero redundancy or unnecessary elaboration.

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

Completeness2/5

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

For a tool with 5 parameters, no annotations, and no output schema, the description is insufficient. It doesn't explain what format the network edges are returned in, how confidence scores should be interpreted, what happens with the 'add_nodes' parameter, or any limitations of the retrieval. The description leaves too many contextual gaps.

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 5 parameters thoroughly. The description adds no parameter-specific information beyond what's in the schema. The baseline score of 3 reflects adequate parameter documentation through the schema alone.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the action ('Retrieve') and resource ('protein-protein interaction network for given proteins'), and specifies the return format ('network edges with confidence scores'). It distinguishes from some siblings like 'get_string_ids' or 'resolve_proteins' by focusing on network retrieval, but doesn't explicitly differentiate from 'get_interaction_partners' which might have overlapping functionality.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives like 'get_interaction_partners' or 'get_ppi_enrichment'. It mentions what the tool does but offers no context about appropriate use cases, prerequisites, or exclusions.

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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