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jean — Molecular Biology & Genomics

notebook_cross_refs

Read-only

Extract @plasmid / !action / &gel cross-references from a lab-notebook markdown body.

Input Schema

TableJSON 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.
body_mdYesthe notebook entry body (markdown).
_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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
gelsYes&gel references
actionsYes!action references
plasmidsYes@plasmid references

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 fully covered without the description. The description adds no behavioral context beyond the parse itself (no note on empty results, malformed tokens, or deduplication), which is the minimum viable level given the annotation coverage.

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 sentence with the verb and the recognized token patterns front-loaded, and zero filler. Nothing is repeated from the schema or annotations.

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?

An output schema exists, so return structure need not be explained, and annotations cover the safety profile. The description is nearly complete for a pure read-only extractor, though it omits any handling notes for malformed or absent reference tokens.

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 adds meaning the schema does not: the recognized cross-reference token syntaxes (@plasmid, !action, &gel). That tells the agent what content in body_md will actually be matched, which is genuinely useful beyond field descriptions.

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 ('Extract') and resource ('cross-references') and even names the exact reference syntaxes (@plasmid / !action / &gel), so an agent knows precisely what this returns. It does not name a sibling, but no other tool in the list appears to perform notebook reference extraction, so differentiation is implicit.

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?

The phrase 'from a lab-notebook markdown body' implies the input context, but there is no explicit when-to-use, when-not-to-use, or prerequisite guidance. An agent is left to infer that this is for parsing notebook entries rather than, e.g., validating them.

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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