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Jean — Molecular Biology & Genomics

add_notebook_figure

Put a drawing that is on screen into the lab notebook as a numbered figure: a chart, gel, map or any other picture a tool drew on the stage.

Input Schema

NameRequiredDescriptionDefault
tabNothe stage tab or the tool surface id it shows (e.g. `qpcr-curves`). Leave it out for the tab the user is looking at.
_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.
captionNoa caption to use instead of the generated one. Leave it out unless the user asked for wording: the generated caption names the drawing, the tool and its reading.
drawingNothe drawing to take, by its name (a chart's title, e.g. "Melt curve"). Leave it out to take the first drawing of the tab.
_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.
entry_idNoappend to this entry instead of the open one; with neither, a new entry is started and named after the drawing.

Output Schema

NameRequiredDescriptionDefault
figureYesits figure number in that entry, as the preview and every export print it
captionYesthe caption written
entry_idYesthe entry the figure went into

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already establish that this is a non-read-only, non-destructive, closed-world write, and the description adds that the result is a 'numbered figure' in the notebook. It does not say whether repeat calls duplicate figures, how numbering is assigned, or what happens when nothing is on the stage - gaps that matter for a writer.

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?

A single front-loaded sentence that defines the action and then spends its remaining words on the one genuinely ambiguous term ('drawing'). Nothing is wasted.

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 all six parameters optional, 100% schema coverage and an output schema present, the description only needs to explain the action and its target, which it does. The default-entry behavior and duplicate handling are left entirely to the schema.

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%, so tab, caption, drawing, entry_id and _subject are all documented in the schema itself. The description adds no parameter-level meaning beyond clarifying conceptually that the source is something on screen; baseline 3 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?

States a specific verb and resource ('put a drawing ... into the lab notebook as a numbered figure') and disambiguates 'drawing' with a concrete enumeration (chart, gel, map, any picture a tool drew on the stage). It does not name or contrast any sibling, but the intent is unmistakable.

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 agent must infer that this follows a tool that drew something on the stage. There is no explicit when-to-use or when-not statement, and no routing to alternatives such as notebook_cross_refs or record_experiment.

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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