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Get a vector with its annotation

vector_library_get
Read-onlyIdempotent

Return one vector from the library: its GenBank accession and version, length, topology, organism/definition, complete sequence, and the full annotated feature table (type, label, 1-based inclusive start/end, strand, spliced length, and the location descriptor as the record wrote it). Accepts the library id, the vector name, or the accession. An unrecognised id is an error carrying the closest names — never an empty result.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesLibrary id (e.g. "pbr322"), vector name ("pBR322"), or accession ("J01749" / "J01749.1").
includeSequenceNoSet false for the annotation only — useful for a large BAC where the bases are not the point.

TDQS

A4.5/5.0
Behavior5/5

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

Annotations already mark the operation read-only and idempotent, and the description adds significant behavioral detail beyond that: exact error semantics, the explicit list of returned fields, and the coordinate/location conventions (1-based inclusive, strand, spliced length, original location descriptor). This is genuinely useful transparency for an agent deciding how to interpret results.

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?

The description is dense but well-structured: it opens with the core action, lists return contents compactly, then covers accepted identifiers and error behavior. Every sentence adds operational value, and nothing is wasted.

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?

For a single-record read operation with no output schema, the description covers all the essentials: what is returned field-by-field, what identifiers are accepted, how errors behave, and the effect of the optional parameter is already in the schema. No critical gap remains for an agent to invoke or interpret the tool correctly.

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?

Input schema coverage is 100%, and the schema already documents both parameters, including examples for id and the use case for includeSequence=false. The tool description reinforces the identifier alternatives but does not add meaning beyond the schema. Baseline 3 is appropriate because the schema carries the parameter documentation burden.

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?

The description states a specific verb and resource ('Return one vector from the library') and enumerates exactly what is included, from accession and sequence to the full feature table. Its singular scope and explicit content list clearly set it apart from sibling search tools like vector_library_search without needing to name them.

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 description clearly indicates when to use the tool: to retrieve a single known vector by library id, name, or accession. It also gives behavioral guidance on error handling — unrecognised ids produce a closest-names error rather than an empty result. It does not explicitly list alternatives or exclusion cases, but the exact-identifier framing is sufficient.

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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TDQS

A3.6/5.0
Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

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