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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.

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.
_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

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

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=true, so safety and external-source behavior are covered. The description adds that results come from NCBI and are complete ('every accession and length NCBI reports'), which is mildly useful, but it says nothing about how many assemblies are returned, how the default 'top' assembly is chosen, or failure modes for ambiguous names.

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 packs the resource, the scope and the returned detail with no filler. It is dense and comma-heavy, but every clause contributes information.

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 values need no explanation, and all five parameters are fully documented in the schema. The description covers the core purpose adequately; only the default-assembly-selection behavior and the distinction from adjacent accession/record lookup tools are left implicit.

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%, so the schema already documents organism name forms, the assembly pin, and the replicons cost trade-off. The description adds nothing parameter-specific beyond the general phrase 'every accession and length.' Baseline 3 applies when the schema does the heavy lifting.

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 gives a specific verb and resource: 'Resolve an organism to its published genome assemblies and the chromosomes, plasmids and organelles each one is made of.' That is concrete and unambiguous about the output shape. It does not name a sibling (e.g. find_accessions, lookup_gene, search_records) to distinguish itself from, so it stops short of a 5.

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?

The use case is implied (you have an organism, you want its assembly accessions and replicon lengths) but the description states no explicit when-to-use, when-not-to-use, or alternative tool. The schema's 'assembly' parameter partially compensates by explaining pinning to a build, but that guidance lives outside the description text.

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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