jean — Molecular Biology & Genomics

fetch_record

Read-only

Fetch a sequence by accession from an authoritative archive (NCBI Nucleotide or Protein, ENA, UniProtKB, the iGEM Registry, Addgene, or the EBI Dbfetch gateway) and hand it downstream as a real record with its annotations. This is how a pipeline starts from a published sequence rather than from whatever happens to be open.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`db`	No	Dbfetch only: which of its databases. Only applies when source is dbfetch.
`_files`	No	The 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.
`format`	No	Dbfetch only: which of that database's formats. Only applies when source is dbfetch.
`source`	No	which archive holds it. Values: ncbi (NCBI Nucleotide), ncbi-protein (NCBI Protein), ena (ENA), uniprot (UniProtKB), igem (iGEM Registry), addgene (Addgene), dbfetch (EBI Dbfetch).	ncbi
`_subject`	No	The 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.
`accession`	Yes	the accession to fetch, e.g. NC_005816, U49845, P38398, BBa_R0040. An NCBI accession may carry a window: `NC_005816 REGION: 5000..7000`.
`record_index`	No	which record to emit when the fetched file holds several (0-based).

Output Schema

TableJSON Schema

Name	Required	Description
`name`	Yes	the record name the archive gave it
`length`	Yes	its length in bases (or residues, for a protein)
`record`	Yes	the fetched sequence, ready for a downstream node's $subject
`circular`	Yes	whether the archive says it is circular
`provenance`	Yes	the archive, the accession, the URL and when it was fetched — what makes the result re-fetchable
`featureCount`	Yes	how many annotations came with it

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4/5.0

Behavior3/5

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

Annotations already cover the safety profile (readOnlyHint, destructiveHint=false, openWorldHint), so the bar is lower. The description usefully adds that the result is materialized as a real record with annotations rather than a raw string, but says nothing about archive unavailability, invalid-accession behavior, or how multiple records are resolved.

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?

Two sentences, front-loaded with the action and its scope; the second sentence earns its place by distinguishing this from the open-record path. No filler.

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, return values need not be explained, and the source list plus record semantics cover the agent's needs. Minor gap: no guidance on choosing among archives when an accession could exist in several, or on failure modes.

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% and every parameter (db, format, source, accession, record_index, _subject, _files) is documented in the schema itself, including the REGION window syntax. The description adds only the archive enumeration, so the baseline 3 applies.

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 (fetch) and resource (a sequence by accession) and enumerates the exact archives it draws from, including the Dbfetch gateway. An agent knows precisely what this produces: a downstream record with its annotations, not raw text.

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

Usage Guidelines4/5

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

The clause 'starts from a published sequence rather than from whatever happens to be open' implicitly routes the agent away from the open-record sibling (get_open_record), but it never names that sibling or states exclusions explicitly. Clear context, no named alternative.

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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