Jean — Molecular Biology & Genomics

build_addgene_deposit

Read-only

Fill Addgene's own deposit spreadsheet from a record: one row per plasmid with its name and sequence, plus your answers for every plasmid (purpose, plasmid type, cloning method, resistance, growth strain and the other drop-downs).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "genbank": "<genbank>"
    },
    "name": "build_addgene_deposit"
  }
}

Input Schema

Name	Required	Description
`_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.
`answers`	No	the sheet's columns to fill for every plasmid, header → value, e.g. {"Purpose": "Expresses EGFP in E. coli", "Bacterial Resistance": "Ampicillin"}. A drop-down column takes one of its own choices; run once without answers to read them from `columns`.
`genbank`	Yes	the plasmids to deposit, as GenBank text: one row per nucleotide record.
`_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.

Output Schema

Name	Required	Description
`file`	Yes	the filled workbook: `name`, and its bytes as `base64`
`columns`	Yes	every column of Addgene's sheet: its header, Addgene's help text, and its choices where it has a drop-down
`reading`	Yes	what was written and what is left for the depositor, generated from the run
`written`	Yes	plasmids written into the sheet
`problems`	Yes	every value left out because the sheet would refuse it, with the plasmid, the column and the reason

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

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 covered, and an output schema exists so return shape needn't be described. The description adds the structural behavior that matters — one row per plasmid, name plus sequence, with per-plasmid answers mapping onto the sheet's columns — but says nothing about what happens with malformed or multi-record GenBank input, or what a drop-down mismatch does.

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 core action first, then the row model, then the answers payload. The parenthetical list of drop-down fields is a little long but each item earns its place by signalling the breadth of required answers.

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?

For a spreadsheet-building tool with a full output schema and 100% parameter coverage, the description supplies what an agent needs: the source record, the one-row-per-plasmid model, and the answers payload. The missing piece is the discovery workflow for drop-down choices, which is only discoverable by reading the 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 baseline is 3; the schema already explains `answers` as header → value with drop-down constraints and defines `genbank`, `_subject` and `_files`. The description reinforces the row-per-record mapping and enumerates the answer categories, which is helpful framing but largely restates what the schema documents.

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?

"Fill Addgene's own deposit spreadsheet from a record" gives a specific verb (fill) and a specific resource (Addgene's deposit spreadsheet), and the possessive "Addgene's own" implicitly separates it from the sibling builders build_ena_submission and build_genbank_submission. It stops short of naming those alternatives outright, so the differentiation is inferential rather than explicit.

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?

Usage is only implied: an agent can infer this is the tool for Addgene deposits rather than ENA or GenBank, but the description never states when to choose it, what prerequisites exist (e.g. needing GenBank text in hand), or how the two-pass answers workflow should be sequenced. The one useful workflow hint (run once without answers to read `columns`) lives in the schema, not the description.

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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