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UCSC Genome Browser MCP Server

by hlydecker
OverviewSchemaRelated ServersScoreDiscussions
Python
Remote

list_chromosomes

Retrieve chromosome lists from UCSC Genome Browser assemblies, hubs, or databases, with optional filtering by specific tracks for targeted genomic analysis.

Instructions

List chromosomes in an assembly hub, track hub, or UCSC database genome. Optionally filter by specific track.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
genomeYesGenome assembly name
hub_urlNoURL of track/assembly hub (optional)
trackNoSpecific track name to list chromosomes from (optional)

Implementation Reference

  • ucsc-genome-mcp.py:189-210 (registration)
    Registration of the 'list_chromosomes' tool, including its input schema definition.
    Tool(
    name="list_chromosomes",
    description="List chromosomes in an assembly hub, track hub, or UCSC database genome. Optionally filter by specific track.",
    inputSchema={
        "type": "object",
        "properties": {
            "genome": {
                "type": "string",
                "description": "Genome assembly name"
            },
            "hub_url": {
                "type": "string",
                "description": "URL of track/assembly hub (optional)"
            },
            "track": {
                "type": "string",
                "description": "Specific track name to list chromosomes from (optional)"
            }
        },
        "required": ["genome"]
    }
),
  • ucsc-genome-mcp.py:393-400 (handler)
    Handler implementation for 'list_chromosomes': constructs parameters (genome, hubUrl, track) and calls the UCSC Genome API endpoint /list/chromosomes.
    elif name == "list_chromosomes":
    params = {
        "genome": arguments["genome"],
        "hubUrl": arguments.get("hub_url"),
        "track": arguments.get("track")
    }
    url = build_api_url("/list/chromosomes", params)
    result = await make_api_request(url)

Tool Definition Quality

B3.2/5.0
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 describes the action of listing chromosomes with optional filtering, but lacks details on permissions, rate limits, output format, or error handling. For a tool with no annotations, this is a significant gap in transparency.

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 and includes key details without waste. It is appropriately sized for the tool's complexity, making it easy to parse and understand 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 no annotations and no output schema, the description is incomplete. It covers the basic action but lacks crucial behavioral context (e.g., response format, error cases) and does not compensate for the absence of structured data. For a tool with 3 parameters and no annotations, this leaves significant gaps in understanding how to 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. The description adds minimal value by mentioning optional filtering by track, which aligns with the 'track' parameter, but does not provide additional syntax, format, or usage details beyond what the schema specifies. Baseline 3 is appropriate as the schema handles most of the parameter documentation.

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 ('chromosomes'), specifying the sources (assembly hub, track hub, or UCSC database genome) and optional filtering by track. However, it does not explicitly differentiate from sibling tools like 'list_ucsc_genomes' or 'list_hub_genomes', which focus on listing genomes rather than chromosomes, leaving some ambiguity in sibling tool distinction.

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

Usage Guidelines3/5

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

The description implies usage by mentioning optional filtering by track, but it does not provide explicit guidance on when to use this tool versus alternatives like 'list_tracks' or 'list_ucsc_genomes'. No exclusions or prerequisites are stated, leaving usage context partially inferred rather than clearly defined.

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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