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get_transcripts

Fetch Ensembl transcripts, canonical isoform, and exon structures by gene ID or symbol to analyze splice variants and coordinates.

Instructions

Fetch transcripts, canonical isoform, and exon structures from Ensembl.

Args: query: Ensembl Gene ID (e.g. ENSG00000141510) or gene symbol (e.g. TP53). species: Species name (default: 'homo_sapiens' or 'mus_musculus').

Returns: JSON string containing gene coordinates and transcript variants with exon models.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
speciesNohomo_sapiens

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv0.7.0

TDQS

B3.3/5.0
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 behavioral burden. 'Fetch' implies a read operation, but the description does not disclose permissions, rate limits, authentication needs, or error behavior. The return information largely duplicates the output schema.

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 and front-loaded: one sentence states the purpose, followed by Args and Returns sections. Every sentence is useful and there is no filler.

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 a simple two-parameter fetch tool with an output schema, the description covers the purpose, both parameters, and the return shape. The main missing piece is usage context relative to sibling tools, which prevents a perfect score.

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?

Schema description coverage is 0%, so the description must compensate, and it does: query is documented as an Ensembl Gene ID or gene symbol with examples, and species is documented with a default and example alternatives. It stops short of clarifying whether species accepts values beyond the two mentioned.

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 uses a specific verb and resource: 'Fetch transcripts, canonical isoform, and exon structures from Ensembl.' It clearly states what data is returned. However, it does not explicitly distinguish this tool from siblings such as resolve_gene or get_protein_info, so it falls short of the top score.

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?

There is no guidance on when to use this tool versus alternatives. It lists arguments and return format but does not mention prerequisites, when-not-to-use cases, or sibling tools like resolve_gene or find_orthologs.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.