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biothings_query_many_genes

Batch query gene annotations by submitting multiple gene IDs or symbols in a single request, retrieving details for each.

Instructions

Batch query genes by multiple terms, returning a list of gene details.

    Perform multiple gene searches in a single request using a comma-separated list of query terms.
    Unlike `query_genes`, the `query_list` parameter takes multiple **terms** (like gene IDs, symbols, names) 
    rather than full query strings. The `scopes` parameter defines which fields these terms should be searched against.
    
    **Endpoint Usage:**
    - Query multiple symbols: `query_list=CDK2,BRCA1` with `scopes=symbol`
    - Query multiple Entrez IDs: `query_list=1017,672` with `scopes=entrezgene`
    - Query mixed IDs/symbols: `query_list=CDK2,672` with `scopes=symbol,entrezgene`
    

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sizeNo
emailNo
fieldsNoall
scopesNoentrezgene,ensemblgene,retired
speciesNo
query_listYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description carries the full burden. It explains the core behavior (batched search, comma-separated terms, scopes) but does not disclose potential limitations such as rate limits, error handling for invalid terms, or authentication requirements. Thus, transparency is adequate but not thorough.

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?

The description is concise, with two paragraphs and bullet examples. It front-loads the purpose. A slight redundancy exists in the first paragraph (repeats 'batch query' idea), but overall it's efficient.

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

Completeness3/5

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

The description provides enough context for using the tool with required parameters and common optional ones, but does not cover all parameters (size, email, species) or error scenarios. Given the output schema exists, return values are not needed, but the description could be more complete regarding optional fields and behavior on failure.

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 0%, so the description must compensate. It explains query_list (comma-separated terms) and scopes (fields to search against) with examples, and hints at fields via default 'all'. However, it does not explain size, email, or species parameters. Overall, it adds meaningful context for the essential parameters but misses several.

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 that this tool performs batch queries for multiple gene terms and returns a list of gene details. It explicitly distinguishes itself from the sibling tool query_genes by noting that query_list takes multiple terms rather than full query strings, and provides concrete examples (e.g., CDK2,BRCA1).

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 includes explicit usage guidelines: it contrasts with query_genes, explains when to use this tool (for multiple terms), and provides endpoint usage examples with different scopes. This helps the agent choose correctly among siblings.

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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