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map_cdna_to_region

Convert cDNA coordinates to genomic coordinates for transcript analysis using Ensembl data. Input transcript ID and cDNA region to get corresponding genomic location.

Instructions

Map cDNA coordinates to genomic coordinates

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesTranscript stable ID
regionYescDNA coordinates (e.g., 100..300)
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 mapping operation but doesn't describe what the mapping entails (e.g., coordinate transformation rules), potential errors, or output format. For a tool with no annotations, this leaves significant behavioral gaps.

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 directly states the tool's purpose without unnecessary words. It's appropriately sized and front-loaded, with no wasted information.

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

Completeness2/5

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

Given the tool's complexity (coordinate mapping with 2 parameters), lack of annotations, and no output schema, the description is insufficient. It doesn't explain what the mapping operation produces, how coordinates are transformed, or any behavioral aspects, leaving the agent with incomplete context for proper use.

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?

The input schema has 100% description coverage, clearly documenting both required parameters ('id' as transcript stable ID and 'region' as cDNA coordinates). The description doesn't add any parameter details beyond what the schema provides, so it meets the baseline of 3 for high schema coverage.

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 'Map' and the resources 'cDNA coordinates to genomic coordinates', making the purpose specific and understandable. However, it doesn't explicitly differentiate from sibling tools like 'map_cds_to_region' or 'map_translation_to_region', which appear to perform similar coordinate mapping operations.

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 like 'map_cds_to_region' or 'map_translation_to_region', nor does it mention prerequisites or exclusions. It simply states what the tool does without contextual usage information.

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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