Skip to main content
Glama
mfiume

Omics AI MCP Server

by mfiume

sql_search

Execute SQL queries against genomics research datasets using Trino syntax to analyze and explore data collections for scientific discovery.

Instructions

Execute a SQL query against a collection using Trino syntax

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
networkYesNetwork name or URL
collection_slugYesCollection slug name
sqlYesSQL query string (use Trino syntax with double quotes for identifiers)
max_pollsNoMaximum number of polling attempts (default: 10)
poll_intervalNoSeconds to wait between polls (default: 2.0)
access_tokenNoOptional access token for authentication
Behavior2/5

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

With no annotations provided, the description carries full burden but only mentions the Trino syntax constraint. It omits critical behavioral details such as authentication needs (implied by access_token parameter but not explained), rate limits, query execution time, error handling, or what happens on failure. This is inadequate for a tool with multiple parameters and potential side effects.

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. Every word earns its place, making it easy to parse quickly while avoiding redundancy or fluff.

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 complexity of executing SQL queries (with 6 parameters, no output schema, and no annotations), the description is insufficient. It lacks information on return values, error conditions, security implications, or how results are formatted, leaving significant gaps for an AI agent to use this tool 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 fully documents all 6 parameters. The description adds minimal value beyond the schema by noting Trino syntax and double quotes for identifiers, but doesn't elaborate on parameter interactions or usage examples. Baseline 3 is appropriate as the schema does the heavy lifting.

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 ('Execute a SQL query') and target ('against a collection'), specifying the syntax ('using Trino syntax'). It distinguishes from siblings like count_rows or get_schema_fields by focusing on query execution rather than metadata retrieval, though it doesn't explicitly contrast with query_table which might be similar.

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?

No explicit guidance on when to use this tool versus alternatives like query_table or other siblings. The description implies usage for SQL queries on collections but lacks context on prerequisites, performance considerations, or exclusions, leaving the agent to infer based on tool names alone.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/mfiume/omics-ai-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server