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PharmGKB Gene Search

pharmgkb.pharmacology.gene_search
Read-onlyIdempotent

Search PharmGKB for a pharmacogenomics gene by HGNC symbol (e.g. CYP2C9, CYP2D6, BRCA1, VKORC1, TPMT). Returns the PharmGKB gene ID, chromosomal location (GRCh38), strand, CPIC/AMP gene status, allele type, VIP tier, and plain-text clinical summary. CPIC genes have validated drug-dosing guidelines. AMP genes are on the AMP Tier I/II actionable list. Source: PharmGKB, CC BY-SA 4.0.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
symbolYesHGNC gene symbol to search for (e.g. CYP2C9, CYP2D6, BRCA1, VKORC1, TPMT). Case-insensitive. Use the official gene symbol as listed by HGNC.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, and non-destructive behavior. The description adds valuable context beyond the annotations by explaining what the returned fields mean (e.g., CPIC genes have validated drug-dosing guidelines, AMP genes are on an actionable list) and stating the source/license. It 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?

Three sentences pack the purpose, key output fields, clinical meaning, and source/licensing without waste. The first sentence front-loads the search semantics and return summary, with supporting context in the next sentences.

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 single-parameter read-only search with an output schema, the description is complete: it identifies the input, previews output fields, explains domain-specific statuses, and states the data source. The output schema covers return structure, so no further return-format detail is needed.

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%, and the schema's parameter description already includes the same examples, case-insensitivity, and HGNC guidance. The tool description only repeats 'by HGNC symbol' and examples, adding no new semantic meaning beyond what the schema provides. Baseline 3 applies because the schema carries the full burden.

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 a specific action ('Search PharmGKB for a pharmacogenomics gene'), the resource (PharmGKB genes), and the key identifier (HGNC symbol). It lists concrete examples and details the returned fields, making it unambiguous and distinct from the sibling drug_search, variant_lookup, and drug_labels tools by resource type.

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 makes the usage context clear: use this tool when you need gene-level pharmacogenomics information by HGNC symbol. It does not explicitly name sibling alternatives or state when-not-to-use, but the resource-oriented wording ('gene') effectively differentiates it from the drug and variant tools in the same pharmgkb namespace.

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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