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antibody_isotype

Read-only

Name the CONSTANT region of an antibody chain: which immunoglobulin gene and allele it carries (IGHG1, IGHA2, IGKC, IGLC2 …), and where each IMGT domain sits on it — CH1, the hinge, CH2, CH3, the secretory tail and the membrane exons, or the single C region of a light chain.

Input Schema

NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
proteinYesthe chain (one-letter amino acids); the constant region in it is found, so a whole heavy chain is fine.
speciesNoonly consider genes of this species, spelled as IMGT spells it (Homo sapiens, Mus musculus). Left out, every species in the catalogue competes and the answer says which won.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
minIdentityNoa domain matching less of its reference than this is not reported.

Output Schema

NameRequiredDescriptionDefault
geneYesthe IMGT gene the constant region matches (IGHG1)
alleleYesthe allele, as IMGT numbers them (01)
domainsYeseach IMGT label placed on the chain: label, start, end (1-based inclusive), identity, coverage
speciesYesthe species whose gene answered
identityYesidentical residues over every aligned column, 0 to 1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile of this analysis is covered without the description. An output schema exists, so return-shape disclosure is also not required here. The description adds only the scoping fact that it works on the constant portion of a chain; it says nothing extra about determinism, database provenance, or ambiguities, so it earns a neutral middle score rather than credit.

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?

A single front-loaded sentence that opens with the core action and then enumerates what gets named. The em-dash list of IMGT domains is long but each item carries information. No filler or marketing language.

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

Completeness3/5

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

The tool takes nested record inputs (_subject, _files) plus species and identity thresholds, and the description covers only what is reported, not the operational context such as what happens with an ambiguous or truncated chain when minIdentity is loose. Because the schema is fully described and an output schema exists, most of the remaining burden is already met, making this adequate but not 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 description coverage is 100%, including the meaningful notes on 'protein' (constant region is located within the chain), 'species' (IMGT spelling; omitting it lets all species compete) and 'minIdentity' (default threshold). The description contributes no parameter meaning beyond that, so the baseline of 3 for a fully documented schema applies.

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 states a concrete verb+resource (name the constant region of an antibody chain) and enumerates the outputs: immunoglobulin gene and allele (IGHG1, IGHA2, IGKC, IGLC2) plus IMGT domain placement (CH1, hinge, CH2, CH3, secretory tail, membrane exons, light-chain C region). An agent can distinguish this from general protein-annotation tools. It stops short of naming the antibody siblings it is closest to (antibody_molecule, number_antibody), so it is clear but not sibling-differentiated.

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 explicit when-to-use or when-not-to-use guidance, and none of the plausible alternatives (antibody_molecule, antibody_canonical_classes, compare_antibodies) are referenced. Usage must be inferred entirely from the phrase 'CONSTANT region', which implies this is for isotype/allotype identification rather than full-chain characterization. That inference is available but not spelled out.

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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