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pharmacogenomics-guidelines-mcp-server

Search alleles

pgx_search_alleles
Read-onlyIdempotent

Inspect CPIC allele function, evidence, definition metadata and complete population frequencies for geneSymbol. Name matches literally first, then a matching gene prefix before a star allele may be removed; clinicalFunctionalStatus matches literal text case-insensitively. Discover genes with pgx_list_reference. Definitions are metadata, not variant interpretation. Frequencies are source fractions; inferred frequencies are not observations and do not establish individual risk. Pages have a 24,000-byte complete-result soft budget; an indivisible exception sets oversizedRow. Continue with page.nextOffset.

Input Schema

NameRequiredDescriptionDefault
nameNoExact source allele name; blank means unset.
limitNoPositive safe-integer row limit; values above 100 are clamped to 100 with a notice (default 25).
offsetNoZero-based offset; use nextOffset to continue (default 0).
geneSymbolYesGene symbol, such as CYP2C19 or HLA-B; outer whitespace is ignored.
clinicalFunctionalStatusNoCase-insensitive literal source clinical functional status; blank means unset.

Output Schema

NameRequiredDescriptionDefault
capNoEffective public page limit.
pageNoSource pagination metadata.
errorNoPresent when the call failed. Absent on success.
itemsNoSource alleles, embedded definitions and population frequencies.
shownNoNumber of returned rows, equal to page.returned.
noticesNoNotices about this result; empty when none apply.
truncatedNoWhether more matching rows remain after this page.
provenanceNoLive source attribution and retrieval details.
oversizedRowNoWhether one complete indivisible row exceeds the soft byte budget.
effectiveQueryNoEffective allele selectors and page bounds.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior5/5

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

Adds substantial behavior beyond the readOnly/idempotent/openWorld annotations: name-matching precedence (literal first, then gene-prefix stripping), case-insensitive clinicalFunctionalStatus matching, a 24,000-byte soft budget with an oversizedRow exception, and nextOffset continuation. It also discloses interpretive caveats (definitions are metadata, inferred frequencies do not establish individual risk).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Purpose is front-loaded, followed by matching rules, interpretive caveats, and pagination guidance in a logical order. Dense but nearly every sentence carries operational or safety value; the prose is slightly telegraphic which costs some readability.

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?

An output schema exists, so return-shape explanation is not needed, and pagination plus the oversizedRow edge case are covered. Filters, matching semantics, and interpretive caveats are all addressed for a fairly complex pharmacogenomic search.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3; the description exceeds that by explaining the cross-parameter matching precedence for name and the case-insensitive literal semantics for clinicalFunctionalStatus. It adds no detail on limit clamping or offset beyond what the schema already states.

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?

Specific verb and resource: it states it inspects CPIC allele function, evidence, definition metadata and population frequencies for a geneSymbol. It differentiates from pgx_list_reference for gene discovery, though it does not distinguish itself from pgx_lookup_diplotype or pgx_search_pairs.

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?

Explicitly routes gene discovery to pgx_list_reference, giving clear context for when this tool is not the right one. It stops short of stating when to prefer pgx_lookup_diplotype or pgx_search_pairs, so alternatives are only partially covered.

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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