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overlap_id

Find genomic features overlapping a specific Ensembl ID to identify intersecting genes, transcripts, variants, or regulatory elements for genomic analysis.

Instructions

Get features that overlap a specific feature by ID

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesEnsembl stable ID
featureNoType of feature to retrievegene
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It states the action 'Get features that overlap', implying a read operation, but doesn't disclose any behavioral traits such as rate limits, authentication needs, error handling, or what 'overlap' means in practice (e.g., genomic coordinates, functional overlap). For a tool with no annotations, this leaves significant gaps in understanding how it behaves.

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 a single, efficient sentence that front-loads the core purpose without any wasted words. It directly states what the tool does, making it easy to parse and understand quickly. Every word earns its place, and there's no redundancy or unnecessary elaboration.

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?

Given the complexity (a read operation with 2 parameters, one with an enum), no annotations, and no output schema, the description is minimally adequate. It covers the basic purpose but lacks details on behavior, output format, or usage context. For a tool with no output schema, it should ideally hint at what 'features' are returned, but it doesn't, leaving the agent to rely on the schema alone for parameters without guidance on results.

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%, with clear descriptions for both parameters: 'id' as an 'Ensembl stable ID' and 'feature' as a 'Type of feature to retrieve' with an enum list. The description adds no additional meaning beyond the schema, such as explaining the relationship between 'id' and 'feature' or providing examples. Since the schema does the heavy lifting, the baseline score of 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Get' and the resource 'features that overlap a specific feature by ID', which is specific and actionable. It distinguishes from siblings like 'overlap_region' and 'overlap_translation' by focusing on ID-based overlap rather than region or translation-based overlap. However, it doesn't explicitly differentiate from all siblings, such as 'get_xrefs_by_gene' or 'lookup_gene_by_id', which also involve ID-based queries but for different purposes.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It doesn't mention when to prefer this over similar tools like 'overlap_region' or 'lookup_gene_by_id', nor does it specify prerequisites or exclusions. The agent must infer usage from the name and schema alone, which is insufficient for optimal tool selection.

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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