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mine_search

Search AllianceMine for genes, proteins, diseases, and biological entities across model organisms using keyword queries to find genomic data and associations.

Instructions

Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesSearch query - keyword, gene symbol, protein name, etc.
typeNoFilter by type: Gene, Protein, Disease, Pathway, etc.
limitNoMaximum results
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. It mentions the search action but lacks behavioral details such as whether it's read-only, how results are returned (e.g., pagination, format), rate limits, or authentication needs. For a search tool with no annotations, this is insufficient to inform the agent adequately.

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 a single, efficient sentence that front-loads the core purpose without unnecessary details. It uses clear language and avoids redundancy, making it easy for an agent to parse quickly.

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?

Given the tool's complexity (3 parameters, no output schema, no annotations), the description is incomplete. It lacks information on behavioral traits, output format, and usage context relative to siblings. For a search tool in a crowded namespace, more guidance is needed to ensure the agent can use it effectively.

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 (query, type, limit). The description adds minimal value by listing entity types (genes, proteins, diseases) that align with the 'type' parameter but doesn't provide additional syntax or constraints beyond what's in the schema, meeting the baseline for high coverage.

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 tool's purpose: 'Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search.' It specifies the verb (search), resource (AllianceMine), and target entities. However, it doesn't explicitly differentiate from siblings like 'mine_query' or 'search_genes' beyond the broader entity scope, which is a minor gap.

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. With many sibling tools (e.g., 'mine_query', 'search_genes', 'search_diseases'), it fails to specify scenarios where this general keyword search is preferred over more specialized tools, leaving the agent without context for selection.

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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