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UCSC Genome Browser MCP Server

by hlydecker
OverviewSchemaRelated ServersScoreDiscussions
Python
Remote

list_hub_genomes

Retrieve available genomes from a specified UCSC Genome Browser track or assembly hub URL to identify compatible genomic datasets for analysis.

Instructions

List all genomes available in a specified track or assembly hub.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
hub_urlYesURL of the track hub or assembly hub

Implementation Reference

  • ucsc-genome-mcp.py:370-373 (handler)
    Handler implementation for the 'list_hub_genomes' tool. It extracts the hub_url from arguments, builds the API URL for '/list/hubGenomes', and makes the request.
    elif name == "list_hub_genomes":
    params = {"hubUrl": arguments["hub_url"]}
    url = build_api_url("/list/hubGenomes", params)
    result = await make_api_request(url)
  • ucsc-genome-mcp.py:130-143 (registration)
    Registration of the 'list_hub_genomes' tool in the list_tools() function, including name, description, and input schema.
    Tool(
    name="list_hub_genomes",
    description="List all genomes available in a specified track or assembly hub.",
    inputSchema={
        "type": "object",
        "properties": {
            "hub_url": {
                "type": "string",
                "description": "URL of the track hub or assembly hub"
            }
        },
        "required": ["hub_url"]
    }
),
  • ucsc-genome-mcp.py:133-141 (schema)
    Input schema definition for the 'list_hub_genomes' tool.
    inputSchema={
    "type": "object",
    "properties": {
        "hub_url": {
            "type": "string",
            "description": "URL of the track hub or assembly hub"
        }
    },
    "required": ["hub_url"]

Tool Definition Quality

C2.9/5.0
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 states the action ('List all genomes') but doesn't cover critical aspects like whether this is a read-only operation, potential rate limits, error handling, or the format of the returned data. This is a significant gap for a tool with no structured safety hints.

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 directly states the tool's purpose without any redundant or unnecessary information. It is appropriately sized and front-loaded, making it easy 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 lack of annotations and output schema, the description is incomplete. It doesn't explain what the output looks like (e.g., list format, fields included) or address behavioral traits like permissions or errors. For a tool with no structured context, this leaves the agent under-informed.

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?

The input schema has 100% description coverage, with the 'hub_url' parameter clearly documented. The description adds no additional meaning beyond what the schema provides, such as examples or constraints on the URL format. Baseline 3 is appropriate since 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 verb ('List') and resource ('genomes available in a specified track or assembly hub'), making the purpose understandable. However, it doesn't explicitly differentiate from sibling tools like 'list_ucsc_genomes' or 'list_genark_genomes', which might serve similar purposes but for different data sources.

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. It doesn't mention prerequisites, exclusions, or compare to siblings such as 'list_public_hubs' or 'search_genome', 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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