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berntpopp
by berntpopp

Resolve Gene or Transcript ID

resolve_transcript
Read-onlyIdempotent

Resolve a gene symbol or Ensembl transcript ID to MetaDome transcript candidates, sorted by protein length with canonical flag. Validate versioned ENST IDs for tolerance landscape queries.

Instructions

Resolve a gene symbol or versioned Ensembl transcript id to MetaDome GRCh37 transcript candidate(s). A gene symbol returns all transcripts sorted by protein length (aa_length descending) with the longest protein-coding entry flagged canonical. A bare ENST id (version suffix required) is validated and echoed directly. Use the canonical_transcript_id with request_tolerance_landscape to start a tolerance-landscape build. Signature: resolve_transcript(query=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesA gene symbol (e.g. TP53) or a versioned Ensembl transcript id (e.g. ENST00000269305.4). Gene symbols are resolved to candidate transcripts; a bare ENST id is validated and echoed.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
hintNo
_metaNo
fieldNo
queryNo
totalNo
messageNo
successYes
retryableNo
candidatesNo
error_codeNo
transcriptsNo
data_versionsNo
recovery_actionNo
recommended_citationNo
canonical_transcript_idNo
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true, openWorldHint=true. The description adds behavioral details like sorting by protein length, canonical flagging, and ENST validation, which go beyond annotations. No 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 a clear first sentence, detailed behavior, usage hint, and signature. Every sentence adds value with no wasted words.

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

Completeness5/5

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

Given the presence of an output schema and comprehensive annotations, the description is complete. It explains the tool's purpose, input behavior, and output usage, with no gaps.

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 coverage is 100%, so baseline is 3. The description adds value by explaining the behavior for each parameter type (gene vs ENST) and the effect of response_mode, going beyond the schema descriptions.

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 the tool resolves gene symbols or transcript IDs to candidate transcripts, differentiating between input types and noting sorting and canonical flagging. It distinguishes itself from siblings by its unique purpose.

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

Usage Guidelines4/5

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

The description explains when to use the tool and provides a usage hint (use with request_tolerance_landscape). It does not explicitly state when not to use it, but the purpose is clear 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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