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berntpopp
by berntpopp

Get Protein Domains

get_protein_domains
Read-onlyIdempotent

List Pfam domains on a transcript's tolerance landscape: domain ID, name, residue positions, meta-domain mapping, and alignment depth. Landscape must be built first.

Instructions

List the Pfam protein domains annotated on a transcript's tolerance landscape: each domain's ID, Name, start/stop residues, whether a meta-domain (homologous) mapping exists, and its alignment depth. Requires a built landscape (call request_tolerance_landscape first). Signature: get_protein_domains(transcript_id=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
transcript_idYesA versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successYes
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
hintNo
candidatesNo
recommended_citationNo
data_versionsNo
transcript_idNo
gene_nameNo
domainsNo
Behavior4/5

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

Annotations already indicate a safe, idempotent read operation. The description adds valuable behavioral context: the requirement for a pre-built landscape and the specific output fields. No contradictions with annotations.

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 two sentences, front-loaded with purpose and output details, followed by a prerequisite and signature. No wasted words, every sentence adds value.

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 complexity, excellent annotations, and presence of an output schema, the description is complete. It explains the purpose, prerequisite, and output fields, which is sufficient for an agent to use the tool correctly.

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 already provides detailed descriptions for both parameters (transcript_id format and resolution, response_mode enum) with 100% coverage. The description adds no additional parameter semantics beyond what the schema offers, thus baseline 3 is appropriate.

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 explicitly states that the tool lists Pfam protein domains on a transcript's tolerance landscape, detailing the exact fields returned (ID, Name, start/stop residues, meta-domain mapping, alignment depth). This clearly distinguishes it from siblings like get_meta_domain or get_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 clearly states the prerequisite of calling request_tolerance_landscape first, which provides context for when to use the tool. However, it does not explicitly mention alternatives or when not to use it, leaving some ambiguity.

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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