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Glama
ZengZichao
by ZengZichao

bacdive_search_16s

Search the BacDive database for 16S rRNA gene sequences by species or genus to support bacterial identification and taxonomic analysis.

Instructions

Search for 16S rRNA gene sequences in the BacDive database by species or genus name. 16S rRNA gene sequences are the gold standard for bacterial phylogenetic identification and taxonomy.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pageNoPage number for pagination (default: 1).
genusNoGenus name (e.g. 'Bacillus'). Optional if species is provided.
speciesNoSpecies name (e.g. 'Escherichia coli'). Optional if genus is provided.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

C2.9/5.0
Behavior2/5

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

No annotations are provided, so the description carries the full burden. 'Search' weakly implies a read-only operation, but nothing is said about pagination limits, whether results are raw sequences or strain-linked records, result caps, or rate limits. The second sentence is educational framing rather than behavioral disclosure.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The purpose is front-loaded in the first sentence with no waste. The second sentence about phylogenetic identification is padding that does not help an agent invoke the tool correctly, so the definition is not maximally tight.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple three-parameter search with fully documented schema fields, purpose and inputs are adequately covered. However, with no output schema and no annotations, the description should still say what a result looks like and how paging behaves; those gaps leave the agent guessing about the return payload.

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 baseline is 3. The description confirms the species/genus name axis, which matches the schema's own field descriptions and examples, but adds no syntax, format, or matching-semantics detail beyond what structured data already supplies.

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 ('Search for 16S rRNA gene sequences in the BacDive database') plus the input axis (species or genus name). The 16S rRNA resource is distinctive enough that an agent can separate it from siblings like bacdive_search_genome or bacdive_search_taxon, though no sibling is named explicitly.

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

Usage Guidelines2/5

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

The description notes the search keys but gives no when-to-use guidance, no exclusions, and no routing against the other nine bacdive_search_* tools. The phylogenetic 'gold standard' sentence is domain rationale, not an invocation condition, so the agent must infer when 16S is preferable to genome or strain search.

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