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berntpopp
by berntpopp

Get Protein Domains

get_protein_domains
Read-onlyIdempotent

List Pfam protein domains annotated on a transcript's tolerance landscape, including domain ID, name, start/stop residues, meta-domain mapping status, and alignment depth.

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
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact
transcript_idYesA versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first.
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, destructiveHint. Description adds useful context: required prior call and details of returned fields (ID, Name, residues, meta-domain, depth). 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.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Reasonably concise: two sentences plus signature. Front-loaded with purpose. Signature is somewhat redundant but helpful.

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?

Missing output schema, but description lists expected output fields. Requires built landscape is clearly stated. For a simple list tool, this is sufficiently complete.

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?

Schema coverage is 100% with descriptions for both parameters. Description adds little beyond the schema: repeats transcript_id guidance and gives signature but no additional semantic value.

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?

Clear verb 'List' and specific resource 'Pfam protein domains on a transcript's tolerance landscape'. Distinguishes from siblings like get_meta_domain or summarize_intolerant_regions by explicitly linking to 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?

Explicitly states prerequisite: 'Requires a built landscape (call request_tolerance_landscape first)'. Provides a signature example. Could be improved by noting when not to use or mentioning alternatives.

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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