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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.

Input Schema

NameRequiredDescriptionDefault
dbNoDbfetch only: which of its databases. Only applies when source is dbfetch.
_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.
formatNoDbfetch only: which of that database's formats. Only applies when source is dbfetch.
sourceNowhich archive holds it. Values: ncbi (NCBI Nucleotide), ncbi-protein (NCBI Protein), ena (ENA), uniprot (UniProtKB), igem (iGEM Registry), addgene (Addgene), dbfetch (EBI Dbfetch).ncbi
_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.
accessionYesthe accession to fetch, e.g. NC_005816, U49845, P38398, BBa_R0040. An NCBI accession may carry a window: `NC_005816 REGION: 5000..7000`.
record_indexNowhich record to emit when the fetched file holds several (0-based).

Output Schema

NameRequiredDescriptionDefault
nameYesthe record name the archive gave it
lengthYesits length in bases (or residues, for a protein)
recordYesthe fetched sequence, ready for a downstream node's $subject
circularYeswhether the archive says it is circular
provenanceYesthe archive, the accession, the URL and when it was fetched — what makes the result re-fetchable
featureCountYeshow many annotations came with it

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.8/5.0
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 and network reach are covered. The description adds real information beyond that: the result arrives as a concrete record carrying its annotations and is meant to be handed downstream, which tells the agent the output is usable by later tools rather than a raw text dump.

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?

One front-loaded sentence with the verb first and the qualifier (by accession, from which archives) following. The parenthetical archive list is long but earns its place by matching the enum; no filler sentences.

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 7 parameters, a nested subject object, and an existing output schema, the description needs only to establish what is fetched, from where, and that the result is a downstream-usable record — all of which it does. Remaining details are fully carried by the schema and output 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 description coverage is 100%, so every parameter including the nested `_subject`/`_files` plumbing and the Dbfetch-only `db`/`format` pair is documented in the schema itself. The description only mirrors the archive list and adds no format, windowing, or record_index guidance beyond what the schema states, so 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 ("Fetch a sequence by accession") and enumerates the archives, which maps directly onto the `source` enum. It is clearly distinguishable from retrieval-ish siblings in spirit, but it never names alternatives such as load_record, get_open_record, find_accessions, or search_records, so the differentiation stays implicit.

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 phrase "from an authoritative archive" and the accession examples imply when this tool applies (you have an identifier and want the canonical record). There is no explicit when-not guidance, no mention of how it differs from loading a local record or searching for accessions first, leaving the agent to infer routing.

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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