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UCSC Genome Browser MCP Server

by hlydecker
OverviewSchemaRelated ServersScoreDiscussions
Python
Remote

list_tracks

Retrieve available data tracks for a specific genome assembly or hub in the UCSC Genome Browser to explore genomic annotations and datasets.

Instructions

List all data tracks available in a specified hub or UCSC database genome.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
genomeYesGenome assembly name
hub_urlNoURL of track/assembly hub (optional, required with genome for hub tracks)
track_leaves_onlyNoOnly show tracks without composite container information

Implementation Reference

  • ucsc-genome-mcp.py:384-391 (handler)
    Handler logic for the 'list_tracks' tool: constructs parameters from arguments (genome, hub_url, track_leaves_only) and makes an API request to the UCSC Genome Browser's /list/tracks endpoint.
    elif name == "list_tracks":
    params = {
        "genome": arguments["genome"],
        "hubUrl": arguments.get("hub_url"),
        "trackLeavesOnly": 1 if arguments.get("track_leaves_only") else None
    }
    url = build_api_url("/list/tracks", params)
    result = await make_api_request(url)
  • ucsc-genome-mcp.py:167-188 (registration)
    Registration of the 'list_tracks' tool in the MCP server's tool list, defining its name, description, and input schema.
    Tool(
    name="list_tracks",
    description="List all data tracks available in a specified hub or UCSC database genome.",
    inputSchema={
        "type": "object",
        "properties": {
            "genome": {
                "type": "string",
                "description": "Genome assembly name"
            },
            "hub_url": {
                "type": "string",
                "description": "URL of track/assembly hub (optional, required with genome for hub tracks)"
            },
            "track_leaves_only": {
                "type": "boolean",
                "description": "Only show tracks without composite container information"
            }
        },
        "required": ["genome"]
    }
),
  • ucsc-genome-mcp.py:170-187 (schema)
    Input schema definition for the 'list_tracks' tool, specifying parameters: genome (required), hub_url (optional), track_leaves_only (optional).
    inputSchema={
    "type": "object",
    "properties": {
        "genome": {
            "type": "string",
            "description": "Genome assembly name"
        },
        "hub_url": {
            "type": "string",
            "description": "URL of track/assembly hub (optional, required with genome for hub tracks)"
        },
        "track_leaves_only": {
            "type": "boolean",
            "description": "Only show tracks without composite container information"
        }
    },
    "required": ["genome"]
}

Tool Definition Quality

C2.9/5.0
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 listing tracks but doesn't describe key behaviors like whether this is a read-only operation, potential rate limits, authentication needs, or what the output format looks like (e.g., list structure, pagination). This leaves significant gaps for an agent to understand how to handle the tool effectively.

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, clear sentence that efficiently conveys the core purpose without any wasted words. It is front-loaded and appropriately sized for the tool's complexity.

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 (3 parameters, no output schema, no annotations), the description is insufficient. It lacks details on behavioral traits, output format, and usage context, making it incomplete for an agent to fully leverage the tool without relying heavily on the schema alone.

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, so parameters are well-documented there. The description adds no additional semantic context beyond implying a scope ('specified hub or UCSC database genome'), which aligns with the schema but doesn't provide extra value. This meets the baseline for high schema 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 action ('List all data tracks') and the resource ('available in a specified hub or UCSC database genome'), making the purpose understandable. However, it doesn't explicitly differentiate this tool from sibling tools like 'list_hub_genomes' or 'list_ucsc_genomes', which might also involve listing operations in similar contexts, so it doesn't reach the highest score.

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, such as 'list_hub_genomes' or 'list_ucsc_genomes', nor does it mention prerequisites or exclusions. It states what the tool does but offers no context for selection among siblings.

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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