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gnomad-genetics-mcp-server

gnomad-genetics-mcp-server: dataframe describe

gnomad_dataframe_describe
Read-onlyIdempotent

List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
canvas_idYesCanvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
tablesNoTables staged on the canvas.

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, indicating a safe, non-mutating operation. The description adds behavioral context about what is returned (row count and column schema per table) and the staging concept, which complements the annotations without contradicting them. It does not mention error cases or side effects, but given the strong annotation coverage, this is sufficient.

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 concise, two sentences total, with the primary purpose and usage in the first sentence and return details in the second. It is front-loaded, avoids redundancy, and every sentence adds essential information without fluff.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple tool with only one parameter and a rich output schema (present though not shown), the description provides complete context: it explains the staging workflow, the source of the canvas_id, the purpose of writing correct SQL, and what the output will contain (row counts and column schema). This is adequate for an agent to know when and how to use it.

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 single parameter canvas_id is already well-described in the schema: 'Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).' The main description repeats this guidance but adds no new semantic details, so it adds minimal value beyond the schema's 100% coverage. This aligns with the baseline for high schema coverage.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool lists tables staged on a canvas with their columns, explicitly tying its purpose to enabling correct SQL for gnomad_dataframe_query. It also distinguishes itself from related tools by referencing the staging tools (gnomad_list_gene_variants, gnomad_search_clinvar) and the downstream query tool, making its role in the workflow unambiguous.

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

Usage Guidelines4/5

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

The description specifies when to use it: after a staging call, and why: to inspect tables before writing SQL for gnomad_dataframe_query. It provides explicit source of the canvas_id. However, it does not explicitly state when not to use it or mention alternative inspection methods, though the context strongly implies this is the standard inspection step.

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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TDQS

A4.2/5.0
Disambiguation5/5

Every tool has a clearly distinct role: specific variant lookup, gene constraint, coverage, ClinVar search, and canvas SQL describe/query. The closest pair, gnomad_get_variant and gnomad_list_gene_variants, is separated by input type and the depth of data returned.

Naming Consistency4/5

Most tools follow a gnomad_<verb>_<object> pattern like get_coverage, get_variant, list_gene_variants, and search_clinvar. The two canvas helpers break this with gnomad_dataframe_describe and gnomad_dataframe_query, but they form a readable and internally consistent sub-pattern.

Tool Count5/5

Seven tools is well-scoped for a gnomAD/ClinVar genetics server. Each tool addresses a distinct query need, and the two dataframe utilities add real analytic value without bloating the API.

Completeness5/5

The surface covers the core read-only workflows: variant lookup, gene variant listing with filters, constraint, coverage, and ClinVar curation. The dataframe query path prevents dead ends when working with large staged result sets.