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gnomad-genetics-mcp-server

gnomad-genetics-mcp-server: dataframe query

gnomad_dataframe_query
Read-onlyIdempotent

Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants). Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sqlYesRead-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants).
canvas_idYesCanvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
rowsNoResult rows (dynamic columns per the SQL projection), capped at the canvas row limit.
errorNoPresent when the call failed. Absent on success.
columnsNoColumn names in the result, in order.
row_countNoNumber of rows the query produced (materialized count).
truncatedNoTrue when the result exceeded the row cap and was clipped.

TDQS

A4.7/5.0
Behavior5/5

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

Annotations already include readOnlyHint=true and idempotentHint=true, but the description adds specific constraints beyond those: 'SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate.' It also mentions the workflow dependency on staging tools, which is valuable behavioral context not captured by annotations. The description does not contradict any annotation.

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 (about 4 sentences), front-loaded with the core purpose, and every sentence adds value: purpose, usage, example use cases, constraints, and prerequisite call. There is no fluff or repetition, making it efficient and well-structured.

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?

Given the tool is a SQL query against staged tables, the description covers all essential context: the staging mechanism (other tools), the required inputs (canvas_id and table_name), the workflow (call describe first), constraints (read-only, rejected functions), and example use cases. The presence of an output schema means detailed return values are not needed. This is complete for a tool of this complexity.

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 both parameters (sql and canvas_id) are fully documented in the schema. The description reinforces their use but does not add new syntactic or semantic details beyond what the schema already provides (e.g., the schema already says 'Read-only SQL SELECT' and 'Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar'). Since the description adds no new parameter-level information, the baseline 3 is appropriate.

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 what the tool does: 'Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants).' It specifies the verb (run), the resource (canvas table), and the scope (read-only SQL SELECT), and differentiates from siblings by naming the staging tools and the specific use cases (ranking, grouping, filtering).

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

Usage Guidelines5/5

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

The description provides explicit when-to-use guidance: 'Use the canvas_id and table_name those tools returned...' and 'Call gnomad_dataframe_describe first to discover staged table and column names.' It also gives explicit exclusions: 'writes, DDL, and file/HTTP table functions are rejected by the canvas gate.' This gives clear alternatives and context without ambiguity.

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.