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Search Markers

search_markers
Read-onlyIdempotent

Search mouse gene markers by symbol, name, or synonym. Exact matches are pinned for quick identification, with optional filtering by marker type.

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
queryYesFree-text query (symbol fragment, name, synonym).
marker_typeNoOptional marker type filter, e.g. 'Gene'.
limitNoMax hits (default 25).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successNo
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
allowed_valuesNo
hintNo
candidatesNo
queryNo
marker_typeNo
totalNo
returnedNo
limitNo
truncatedNo
resultsNo
Behavior5/5

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

Annotations already indicate read-only, non-destructive, idempotent, and open-world properties. The description adds valuable behavioral context: exact hits are pinned first, results include a truncation contract with next_commands, and marker_type filtering is supported. No contradictions.

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 front-loaded with the core purpose, provides a clear signature, and uses concise, well-structured sentences. Every sentence adds value 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 the complexity of free-text search with ranking, pinning, and truncation, the description covers key aspects: search scope, result ordering, truncation contract, response modes, and linkage to alternative tools. It provides sufficient context for an agent to understand when and how to invoke 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?

Schema description coverage is 100%, so baseline is 3. The description mentions marker_type optional restriction and lists signature, but does not add significant meaning beyond the schema. The description focuses more on output behavior than parameter semantics.

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 it performs free-text search over marker symbols, names, and synonyms with relevance ranking. It explicitly distinguishes itself from sibling tools by specifying it is nomenclature-only and directs to alternative tools for phenotype-driven discovery or exact resolution.

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 guidance on when to use this tool (free-text search) and when not to (phenotype-driven discovery, exact symbol/id), naming specific alternatives like search_phenotype_terms, find_markers_by_phenotype, and resolve_marker.

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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