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uniprot_get_cross_refs

Read-only

Retrieve cross-references to external databases like PDB, Pfam, ENSEMBL, Reactome, KEGG, and STRING for a UniProt accession, with optional database filter.

Instructions

Get cross-references to PDB, Pfam, ENSEMBL, Reactome, KEGG, STRING, etc. Optional database filter.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYes
databaseNo
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

Annotations declare readOnlyHint=true, so no contradiction. The description adds the 'database filter' behavior and examples of databases, but does not discuss rate limits, return format, or other beyond-annotation traits.

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 sentence that front-loads the purpose and includes key specifics. No redundant information, though it could optionally list more databases or structure the filter mention.

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?

Given the output schema exists, the description does not need to explain returns. However, it could mention that 'accession' is a UniProt ID, or list possible response_format values. The examples are helpful but the description feels minimally complete for a tool with many 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?

With 0% schema description coverage, the description must compensate. It only explains the 'database' parameter ('Optional database filter'). It does not explain 'accession' (required) or 'response_format', leaving meaningful gaps.

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 cross-references to multiple databases (PDB, Pfam, etc.) and mentions an optional database filter. It is specific enough to distinguish from many sibling tools like uniprot_get_entry, though it does not explicitly contrast with resolve tools.

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 such as uniprot_resolve_pdb or uniprot_search. The optional database filter is mentioned but not in the context of when to apply it or when not to use this tool.

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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