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uniprot_get_cross_refs

Read-only

Retrieve all curated external-database cross-references for a UniProt entry, optionally filtered by a specific database like PDB or Pfam.

Instructions

List every external-database cross-reference UniProt has curated for an entry (PDB, Pfam, Ensembl, Reactome, KEGG, STRING, and dozens more), optionally narrowed to one database. For the common single-database cases there are dedicated, richer tools that resolve structured details beyond a bare ID: uniprot_resolve_pdb (structures with method/resolution), uniprot_resolve_alphafold, uniprot_resolve_interpro, and uniprot_resolve_chembl. Use this tool for any other database or to see the full cross-reference set at once.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
databaseNoOptional exact database name to filter to, e.g. 'PDB', 'Pfam', 'Ensembl', 'Reactome', 'KEGG', 'STRING'. Leave empty to return cross-references to every linked database.
accessionYesUniProt accession, e.g. 'P04637' (human TP53) or 'P38398' (human BRCA1). Both reviewed (Swiss-Prot) and unreviewed (TrEMBL) accessions are accepted; case-sensitive.
response_formatNo'markdown' (default) for a human-readable report with a provenance footer, or 'json' for a machine-parseable structured payload with the same data. Any other value is rejected.markdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations already declare readOnlyHint and openWorldHint. The description adds context about output formats (markdown with provenance footer, JSON payload) and the scope of data (every external-database cross-reference). It does not contradict annotations, and the additional behavioral details are valuable but not extensive.

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 two sentences with no waste. The first sentence states the core function, and the second provides usage guidance and alternatives. It is front-loaded and every sentence earns its place.

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?

Given full schema coverage, annotations (readOnlyHint, openWorldHint), an output schema (exists), and clear guidelines for use, the description is complete. It tells exactly what the tool does, when to use it, and refers to richer alternatives. No missing information for an AI agent to select and invoke correctly.

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 coverage is 100%, so baseline is 3. The description adds significant value by explaining the purpose of the database parameter (filtering) with examples, clarifying the accession parameter format with specific examples (P04637, P38398) and case-sensitivity, and detailing the response_format options (markdown vs JSON with descriptions). This goes beyond the schema descriptions.

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 lists all external-database cross-references for a UniProt entry, with optional filtering by database. It distinguishes itself from dedicated richer tools for common databases like PDB, AlphaFold, InterPro, and ChEMBL, making the purpose highly specific and unambiguous.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly tells when to use this tool (for databases not covered by dedicated tools or to see the full set) and when not to (for common databases where dedicated tools provide richer details). It names specific alternative tools, providing excellent guidance.

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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