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search_rhea_entity

Find biochemical reactions in the Rhea database by keyword. Retrieve reaction identifiers and equations.

Instructions

Search Rhea database for biochemical reactions using keyword search.

Args: query (str): Search query string. Examples: - "ATP" - find reactions involving ATP - "glucose" - find reactions with glucose - "uniprot:*" - reactions with UniProt annotations - "" - retrieve all reactions Accepts aliases: search, term, keyword, keywords, search_term, name. limit (int, optional): Maximum number of results. Defaults to 100.

Returns: List[Dict[str, str]]: List of reactions, each containing: - 'rhea_id': Reaction identifier (e.g., "RHEA:10000") - 'equation': Reaction equation text

Example: >>> results = search_rhea_entity("ATP", limit=5) >>> for reaction in results: ... print(f"{reaction['rhea_id']}: {reaction['equation']}")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryNo
limitNo
searchNo
termNo
keywordNo
keywordsNo
search_termNo
nameNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations provided, the description fully carries the burden of behavioral disclosure. It explains that the tool returns a list of dictionaries with 'rhea_id' and 'equation', describes the default limit, and shows an example. This gives the agent a clear understanding of the tool's behavior without 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 well-structured with 'Args', 'Returns', and an 'Example' section. Every sentence provides value, and the format is compact and easy to parse. No unnecessary text.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (8 parameters, but most are aliases) and presence of an output schema, the description adequately covers the key aspects: purpose, parameters, and return format. However, it omits potential error cases or pagination details, which would bring it to a 5.

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?

The schema has 0% description coverage, so the description must compensate. It adds meaning for the 'query' parameter with examples and alias names, and for 'limit' with default value. While the aliases are listed as separate schema properties, the description groups them, adding clarity beyond the raw 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 specifies the tool's action ('Search') and resource ('Rhea database for biochemical reactions using keyword search'). It distinguishes itself from sibling tools like search_reactome_entity by naming the specific database and the type of data (biochemical reactions).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides example queries and explains alias parameters, but it does not explicitly state when to use this tool over alternatives (e.g., search_reactome_entity) or when not to use it. The examples imply usage context, but explicit guidance is missing.

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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