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tc2fh

reactome-db-mcp

by tc2fh

search_by_name

Search Reactome database objects by their display name. Supports filtering by class, limiting results, and anchored prefix matching for faster queries.

Instructions

Search objects by _displayName.

Args:
    query: Text to look for in the display name.
    classes: Optional `_class` filter, e.g. ["Pathway", "Reaction"].
    limit: Max results (1-200, default 25).
    anchored: If True, match `name LIKE 'query%'` (fast — uses the prefix
        index). If False (default), match `'%query%'` — more thorough but a
        full scan of the 1.86M-row supertable (~1-2s). There are no FULLTEXT
        indexes, so prefer `anchored=True` and/or a `classes` filter for hot
        paths.

Returns:
    Dict `{count, anchored, results: [{DB_ID, _class, _displayName, stable_id}]}`.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
classesNo
limitNo
anchoredNo
Behavior5/5

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

Despite no annotations, the description fully discloses behavior: it performs a search on a 1.86M-row supertable, describes the two different query modes (prefix vs substring) and their performance, and details the return structure. 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 concise and well-structured: a brief intro, a clear bulleted list of arguments with explanations, and a return format. Every sentence adds value; no redundant or missing information.

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 4 parameters and no output schema, the description is fully complete. It covers argument details, performance, return format, and gives practical advice. The return dict structure is explicitly listed, compensating for the missing output schema.

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?

With 0% schema description coverage, the description compensates by explaining all four parameters (query, classes, limit, anchored) with their default values, constraints, and behavioral implications. This adds significant meaning beyond the schema.

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 searches objects by `_displayName` with a clear verb and resource. It distinguishes from siblings like get_object (which retrieves by ID) and get_participants (which retrieves by specific relationships).

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 the anchored parameter, performance implications, and recommendations for hot paths. It also notes the absence of FULLTEXT indexes, helping the agent decide between anchored=True vs anchored=False and using classes filter.

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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