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berntpopp
by berntpopp

Resolve Gene or Transcript ID

resolve_transcript
Read-onlyIdempotent

Resolves a gene symbol to candidate transcripts with the longest protein-coding flagged canonical, or validates a versioned Ensembl transcript ID for use in tolerance landscape builds.

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
Behavior5/5

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

The description adds significant behavioral context beyond annotations: it specifies resolution to GRCh37, sorting by protein length, flagging longest as canonical, validation of bare ENST id, and response mode verbosity. Annotations already indicate readOnlyHint and idempotentHint, but the description enriches understanding of the tool's behavior.

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 concise with four sentences, each adding distinct value: main action, input details, suggested follow-up, and signature. It is front-loaded and no sentences are redundant or wasteful.

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 tool's simplicity and lack of output schema, the description covers input types, processing details, response modes, and a clear usage hint for downstream tools. It is fully adequate for the tool's complexity.

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 the baseline is 3. The description adds value by elaborating on the query parameter's behavior (gene symbol vs ENST id processing) and the signature line explicitly shows parameter names. It slightly exceeds the baseline.

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 it resolves a gene symbol or versioned Ensembl transcript ID to MetaDome GRCh37 transcript candidates. It distinguishes between input types (gene symbol vs bare ENST id) and mentions the canonical transcript flag. This is a specific verb+resource action with clear differentiation from siblings like request_tolerance_landscape.

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 provides explicit context for when to use the tool (to get transcript candidates and canonical transcript) and suggests a follow-up tool (request_tolerance_landscape). It does not explicitly state when not to use it, but the context is sufficient for an agent to decide.

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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