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biobtree_entry

Get full details for one identifier.

SYNTAX: biobtree_entry(identifier="ID", dataset="dataset_name")

USE FOR:

  • See all attributes of an entry

  • Discover filterable fields

  • Get detailed info (sequences, scores, descriptions)

  • DISCOVER CONNECTIONS: xrefs show what datasets link to this entry

WORKFLOW: Get entry → see xrefs → check EDGES for where they lead → follow relevant paths

RETURNS: All attributes + xref counts to connected datasets

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
datasetYesThe dataset containing the entry
identifierYesThe identifier to look up

TDQS

A4.1/5.0
Behavior4/5

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

No annotations are provided, so the description bears full responsibility. It discloses what the tool returns ('All attributes + xref counts to connected datasets') and outlines a workflow (entry → xrefs → edges). This gives the agent a clear model of the operation's behavior, though it doesn't address error cases or permissions.

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?

The description is organized into clear sections (SYNTAX, USE FOR, WORKFLOW, RETURNS), making it scannable. It is concise enough for the information it conveys, with no redundant sentences.

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?

Given the two required parameters and no output schema, the description covers usage, workflow, and return value shape. It even hints at how to use xrefs to discover connections, which is useful for an AI agent. It could be improved by mentioning error behavior, but overall it is complete for a simple lookup tool.

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?

The schema already describes both parameters ('The dataset containing the entry' and 'The identifier to look up'); the description's syntax line adds a concrete example but no additional semantic depth. With 100% schema coverage, the baseline 3 is appropriate.

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 opens with 'Get full details for one identifier,' clearly stating the tool's action and target. The 'USE FOR' list expands on this with specific use cases (attributes, filterable fields, detailed info, connections). While it doesn't explicitly differentiate from siblings, the purpose is unambiguous and distinct from search/map/atlas.

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 'USE FOR' section provides explicit use cases for when to employ this tool, such as seeing all attributes or discovering xref connections. However, it does not mention when to avoid this tool or name alternative tools like 'biobtree_search' for when the identifier is unknown.

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

A4.4/5.0
Disambiguation5/5

Each tool has a distinct role: atlas for curated summaries, entry for full entry details, map for identifier mapping, and search for cross-database discovery. The descriptions clearly delineate when to use each, with workflow examples reducing any potential confusion.

Naming Consistency4/5

All tool names share the 'biobtree_' prefix and use lower_snake_case. The suffixes mix nouns (atlas, entry) and verbs (map, search), but this is consistent with their function and does not hinder readability or predictability.

Tool Count5/5

Four tools provide a well-scoped abstraction over 70+ databases. Each tool covers a distinct necessity: discovery, mapping, detailed lookup, and curated summaries. This is a solid, minimal set for the stated purpose.

Completeness5/5

The tool surface covers the full lifecycle of biological data exploration: search to find identifiers, map to translate between databases, entry to inspect connections and attributes, and atlas for citable summaries. No obvious dead ends; the workflow examples ensure agents can traverse the data graph effectively.

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