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submit_ncbi

Submit an NCBI accession to antiSMASH for secondary metabolite biosynthetic gene cluster analysis; the sequence is retrieved automatically and a job ID is returned.

Instructions

Submit an NCBI accession number to antiSMASH for secondary metabolite biosynthetic gene cluster analysis. antiSMASH will retrieve the sequence from NCBI automatically. Returns a job ID that can be used to check status and retrieve results.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
emailNoOptional email address for notifications.
strictnessNoDetection strictness level.relaxed
server_typeNoType of antiSMASH server to use.bacteria
extra_featuresNoExtra features to enable (see submit_sequence).
ncbi_accessionYesNCBI accession number of the desired sequence (e.g., NC_003888.3, GCF_000005845.2).

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.6/5.0
Behavior3/5

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

With no annotations, the description carries the full behavioral burden. It usefully discloses that antiSMASH fetches the sequence automatically and that the call is asynchronous (returns a job ID for later status/results), but it omits submission-side traits such as rate limits, external dependency handling, or whether email notification changes behavior.

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?

Three sentences, each earning its place: purpose, automatic retrieval behavior, and async return contract. It is front-loaded and has 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?

For a 5-parameter async submission tool with no output schema and no annotations, the description is largely complete: it explains the automatic sequence retrieval and the job-ID return that links to the check/retrieve siblings. It would be stronger if it named the polling/workflow siblings or noted external-service caveats.

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 all five parameters are already documented in the schema, including enums and defaults. The description adds no syntax, format, or constraint guidance beyond 'NCBI accession number,' 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?

The description states a specific verb (submit), resource (NCBI accession number), target service (antiSMASH), and domain (secondary metabolite BGC analysis). It is clear what the tool does, though it never explicitly contrasts itself with the sibling submit_sequence, which is the obvious alternative.

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 implied by the framing: use this when you have an NCBI accession rather than a raw sequence, and the last sentence gestures at the downstream workflow (check status, retrieve results). However, it gives no explicit when-to-use rule, no exclusion, and never names the alternative submit_sequence.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.