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Jean — Molecular Biology & Genomics

export_construction_record

Read-only

Write a construct's recorded build out as a document: a methods section, a step spreadsheet, the full decoded record, the molecule carrying its own history as GenBank qualifiers, the whole strategy as an OpenCloning document, the runnable QUEEN script that rebuilds it, or the build as an SBOL 2 document.

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.
formatNowhich document to write. `methods` is the default because it is the panel’s first row and the only one every source can produce; the other six each need something of the record, and asking for one a source cannot carry is refused by name rather than answered with an empty file. Values: methods (Methods (Markdown)), steps_csv (Steps (CSV)), record_json (Full record (JSON)), genbank (GenBank with construction history), opencloning (OpenCloning document (JSON)), queen_script (Reconstruction script (Python)), sbol (SBOL 2 construction record).methods
_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.
documentNoFile id or name. The focused document when omitted, exactly as the panel.
sbol_syntaxNowhich RDF syntax to write the SBOL record in. SBOL is RDF and the six concrete syntaxes encode ONE graph, so this changes how the document is written down and never what it says. `rdfxml` is the default because it is what the writer composes and what libSBOLj validates; the rest are re-serialised from that exact document. Ignored unless `format` is `sbol`, and saying so is refused rather than silently dropped. Values: rdfxml (RDF/XML), turtle (Turtle), ntriples (N-Triples), nquads (N-Quads), trig (TriG), jsonld (JSON-LD). Only applies when format is sbol.rdfxml

Output Schema

NameRequiredDescriptionDefault
textYesthe document itself, byte for byte what the panel’s download writes
formatYesthe format actually written: echoed because it is defaulted, not required
sourceYeswhich of the 5 records this was written from: the workbench log, a SnapGene .dna reaction graph, a QUEEN build script, an OpenCloning strategy, or an SBOL 2/3 construction record
syntaxYesthe RDF syntax the SBOL record was written in, echoed because it is defaulted. Empty for every other format, which do not have one
cautionYeswhat the panel warns about after this write, when it warns. Empty is the healthy case: a GenBank whose construct carries no other annotation will not read its own history back, and the file looks perfect either way
filenameYesthe name the panel saves it under, so a pipeline writing several agrees with it
availableYesthe formats THIS record can produce, and for each one it cannot, why: the panel’s own enabled/disabled derivation, so a pipeline can branch on it instead of failing

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.5/5.0
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 is covered without description help. The description adds that outputs are derived artifacts (GenBank qualifiers, OpenCloning JSON, a runnable QUEEN script) but says nothing about size, latency, or what happens when the record lacks construction history — details that actually live in the schema's refusal note.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

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

It is a single front-loaded sentence with the verb first, which is good structure. However, the seven-item enumeration largely duplicates the already verbose `format` enum descriptions in the schema, so a meaningful share of the sentence does not earn its place.

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?

With an output schema present and 100% parameter coverage, the description only needs to establish purpose and the format space, and it does both. The remaining gap — when to prefer this over the history/verification siblings — is minor for a read-only exporter.

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, but the description goes slightly further by mapping each prose artifact ('a step spreadsheet', 'the molecule carrying its own history as GenBank qualifiers', 'the runnable QUEEN script that rebuilds it') onto the enum values, giving an agent an intuitive read on format choices. It says nothing about _subject, document, or sbol_syntax, which are left entirely to the schema.

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 uses a specific verb+resource ('Write a construct's recorded build out as a document') and enumerates the seven concrete artifacts produced, which is distinctive among siblings like get_construction_history or build_assembly_report. It stops short of naming a sibling to contrast with, so an agent must still infer the boundary from the format list alone.

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

Usage Guidelines3/5

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

Usage is only implied: the phrase 'recorded build' suggests this is a post-assembly export step, but there is no explicit when-to-use versus get_construction_history, history_protocol, or compare_constructions. The real routing guidance (methods is the only format every source can produce; unsupported formats are refused by name) lives in the schema, not the description.

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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