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ebi-pdbe-unip_map_ent_unip_map_id_entity_id_ce7aaa0c

Read-only

Retrieve UniProt mappings for a PDB entity ID, including matched accessions, residue-level alignment ranges, and the Best Chain ID to link structural entities with UniProt entries.

Instructions

Returns UniProt mappings for a specific PDB Entity ID, including matched UniProt accessions, residue-level alignment ranges, and metadata identifying the corresponding Best Chain ID for the mapping.

Input Schema

NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered and the bar is lower. The description adds genuine value by disclosing the shape of the result (accessions, alignment ranges, Best Chain ID), which matters because there is no output schema, but it does not address the oddly declared idempotentHint=false on what appears to be a pure lookup.

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?

A single front-loaded sentence with no filler, and the resource being returned is named first. It is dense but every clause carries information about the returned content rather than padding.

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?

With no output schema, the description does its main duty by summarizing the return fields, which is a real contribution. It still leaves gaps for a two-parameter lookup: no indication of what happens with an unmapped entity, whether multiple mappings can be returned, or how the Best Chain ID relates to other chain-scoped tools.

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%, and both required parameters (pdb_id, entity_id with its numeric pattern) are documented in the schema. The description only reinforces that entity_id is the scoping key for the mapping; it adds no format, validity, or edge-case detail beyond the structured fields, 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 and resource: 'Returns UniProt mappings for a specific PDB Entity ID', and enumerates the payload (accessions, residue-level alignment ranges, Best Chain ID metadata). It does not distinguish itself from lookalike siblings such as unip_giruiru, unip_ipuipu, or maps, so an agent must infer the split from names alone.

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?

There is no guidance on when to choose this tool over the many other entity-scoped endpoints (sec_struct, doms, chains, var, annot) or over the other UniProt-oriented tools. No prerequisites or exclusions are stated; the usage context is only implied by the phrase 'PDB Entity ID'.

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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