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uniprot-mcp

uniprot-mcp

by fzlzjerry
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

map_ids

Map identifiers between databases via UniProt's async ID-mapping service. Returns matched pairs and unmapped input IDs.

Instructions

Map identifiers between databases via UniProt's async ID-mapping service.

Submits a job, polls until it finishes, then returns the mapped pairs plus any unmapped input ids. When to_db is 'UniProtKB'/'UniProtKB-Swiss-Prot' each result is enriched with the protein name, entry name, and organism. Use 'UniProtKB_AC-ID' as from_db when starting from UniProt accessions. Validates the database pair against the live UniProt config and, on an invalid value, returns the allowed databases.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "from_db": "<from_db>",
      "to_db": "<to_db>",
      "ids": "<ids>"
    },
    "name": "map_ids"
  }
}

Input Schema

NameRequiredDescriptionDefault
from_dbYesSource database id, e.g. 'UniProtKB_AC-ID', 'Gene_Name', 'RefSeq_Protein', 'Ensembl', 'PDB', 'GeneID', 'KEGG'. An invalid value returns the full allowed list.
to_dbYesTarget database id, e.g. 'UniProtKB' (enriched entries), 'PDB', 'Ensembl', 'KEGG', 'RefSeq_Protein'.
idsYesOne id (string) or many (list), e.g. ['P38398', 'P04637'].

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.4/5.0
Behavior4/5

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

No annotations provided, so description bears full burden. It discloses async behavior, enrichment condition for certain to_db values, and validation feedback (returns allowed databases on invalid value). It doesn't mention rate limits or auth, but the context is adequate for a data mapping tool.

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 three sentences, front-loaded with the core purpose. Every sentence adds value: purpose, workflow details, and validation behavior. No wasted words.

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 presence of an output schema, the description sufficiently covers what the tool does and returns. It explains the async polling and enrichment for certain target databases. Could be slightly more detailed about the response format, but overall complete.

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

Parameters4/5

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

Schema description coverage is 100%, so baseline is 3. The description adds operational context (async nature, enrichment, validation) beyond the schema's parameter descriptions, enhancing understanding of how the tool uses the parameters.

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 clearly states the tool maps identifiers between databases using UniProt's async ID-mapping service. It specifies the verb 'map' and the resource 'identifiers between databases', distinguishing it from sibling tools like get_entry or search_uniprotkb.

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 explains the async workflow (submits job, polls, returns results) and gives a specific usage hint ('Use 'UniProtKB_AC-ID' as from_db when starting from UniProt accessions'). It also describes validation behavior. However, it does not explicitly state when not to use this tool or point to alternatives.

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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