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jean — Molecular Biology & Genomics

by io.github.genmnz
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find_assemblies

Read-only

Resolve an organism to its published genome assemblies and the chromosomes, plasmids and organelles each one is made of, with every accession and length NCBI reports. This is how a pipeline starts from a SPECIES rather than from an accession somebody looked up by hand: hand the replicon accession it returns to fetch_record, with a region, to pull a window of that chromosome. Assemblies come back reference-first, so the default pick is the canonical genome.

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.
_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.
assemblyNoan assembly accession to take the replicons of, instead of this organism's top one. Use it to pin a pipeline to one genome build rather than to whatever is reference today.
organismYesa scientific name, a common name, or a taxonomy id (NCBI Datasets accepts all three). "Escherichia coli", "human", "559292" are all valid.
repliconsNolist the chosen assembly's assembled molecules too. Off costs one request and answers 'which assemblies exist'; on costs two and answers 'which chromosome do I fetch'.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
lengthYesthat replicon’s length in bases, so a region can be chosen against a real span
assemblyYesthe chosen assembly accession: the one asked for, else this organism’s reference-first top hit
organismYesthe assembly record's own organism name, canonical rather than the words that were typed
accessionYesthe largest replicon's nucleotide accession: for most genomes the main chromosome, and what a fetch_record node's $accession wants
repliconsYesthe chosen assembly's assembled molecules (accession, name, length and molecule type), or empty when replicons were not asked for
assembliesYesevery current assembly NCBI publishes for the organism: accession, RefSeq or GenBank, assembly level, organism, tax id, release date and total length

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.6/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true and destructiveHint=false, so safety is covered. The description adds real behavior beyond that: reference-first result ordering, the canonical-genome default, and the request-cost tradeoff for the replicons flag.

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?

Three sentences, front-loaded with what it returns before moving to usage and defaults. Slightly discursive phrasing ('This is how a pipeline starts from a SPECIES rather than from an accession somebody looked up by hand') costs a little, but every sentence adds usable information.

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

Completeness5/5

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

With an output schema present, return values need not be explained, and the description covers the remaining agent needs: entry point, result ordering, default selection, and the follow-on tool call. Nothing required to call it correctly is missing.

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% and the schema descriptions are already rich, so the baseline is 3. The description lifts it by explaining intent: 'assembly' pins a pipeline to one genome build, and 'replicons' on/off answers different questions at different request costs.

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?

States a specific verb+resource ('Resolve an organism to its published genome assemblies') and enumerates the returned content (chromosomes, plasmids, organelles, accessions, lengths). It clearly distinguishes itself from accession-based retrieval tools by naming the workflow it starts and the sibling (fetch_record) it hands off to.

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

Usage Guidelines5/5

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

Explicitly frames the when: start from a SPECIES rather than a hand-looked-up accession, and route the returned replicon accession into fetch_record with a region. It also documents the selection default ('Assemblies come back reference-first, so the default pick is the canonical genome'), leaving little to inference.

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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