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Search Markers

search_markers
Read-onlyIdempotent

Search mouse marker symbols, names, and synonyms with relevance ranking. Pins exact symbol matches for key genes, supporting optional marker type filters.

Instructions

Free-text search over mouse marker symbols, names, and synonyms (FTS, relevance-ranked). Returns ranked {mgi_id, symbol, name, marker_type, score, match} summaries. Exact symbol/synonym hits are PINNED first (match: exact_symbol|exact_synonym|fts) so an exact gene is never buried under transgenes or lncRNAs. Returns a truncation contract {total, returned, limit, truncated}; when truncated, next_commands includes a widen step. marker_type optionally restricts to a type (e.g. 'Gene'). Nomenclature-only: no phenotype semantics — use search_phenotype_terms + find_markers_by_phenotype for phenotype-driven discovery, or resolve_marker for an exact symbol/id. Signature: search_markers(query, marker_type=, limit=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax hits (default 25).
queryYesFree-text query (symbol fragment, name, synonym).
marker_typeNoOptional exact marker-type filter (case-insensitive). One of the MGI marker types; an unrecognised value is rejected with invalid_input.
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact
Behavior4/5

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

Annotations already indicate readOnlyHint=true, destructiveHint=false, and idempotentHint=true, so the description's job is to add operational details. It does so by explaining exact-match pinning, truncation contracts with next_commands, and relevance ranking. This adds significant transparency beyond annotations, though it could mention response_mode behavior more explicitly.

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, using only a few sentences to convey purpose, behavior, exclusions, and signature. It is front-loaded with the core function and efficiently uses space without redundancy.

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 no output schema, the description fully describes the return format (ranked summaries and truncation contract) and the effect of the marker_type filter. It also mentions response_mode verbosity. Combined with rich annotations, the description is complete for agent understanding.

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

Parameters5/5

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

Schema coverage is 100%, but the description adds substantial meaning beyond schema: it explains the pinning behavior based on query, the truncation contract, the marker_type filter effect, and lists the response fields. It also provides the function signature, making parameter usage very clear.

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 performs free-text search over mouse marker symbols, names, and synonyms with relevance ranking and pinning of exact matches. It distinguishes from sibling tools by specifying it is nomenclature-only, explicitly naming alternatives like search_phenotype_terms and resolve_marker for phenotype and exact lookups.

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 explicitly states when to use (free-text nomenclature search) and when not to use (no phenotype semantics), providing alternative tool names and their purposes. This gives clear guidance against misuse.

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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