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microbiomedata

nmdc-mcp

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get_entity_by_id

Retrieve any NMDC entity, such as biosamples, studies, or data objects, by providing its unique ID.

Instructions

Use this tool to retrieve any NMDC entity by its ID. Works with biosamples, studies, data objects, and other NMDC entities.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
entity_idYes
Behavior2/5

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

No annotations provided, so description bears full burden. It discloses the tool retrieves entities but omits critical behavioral traits: return format, error handling, authentication needs, rate limits, or whether it is a read-only operation.

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?

Single sentence that directly states purpose. No unnecessary words, front-loads the action and entity scope. Highly efficient for a simple tool.

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

Completeness2/5

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

For a one-parameter tool with no output schema and no annotations, the description is too sparse. It lacks context on output behavior, error responses, and when this tool is appropriate relative to siblings.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, but description adds no parameter-specific details. It mentions the tool works with various entity types but does not clarify the expected format or constraints of entity_id beyond the schema type 'string'.

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 clearly states the tool retrieves an NMDC entity by ID and lists examples (biosamples, studies, data objects). However, it does not distinguish from siblings like get_entity_by_id_with_projection which adds projection capabilities.

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?

No guidance on when to use this tool versus alternatives. No mention of prerequisites, limitations (e.g., fetch size), or when to prefer other tools from the sibling list.

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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