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Resolve Gene by Cross-Reference

resolve_gene_by_xref
Read-onlyIdempotent

Resolve any external gene identifier from databases like Ensembl or UniProt to its official HGNC gene symbol. Provide the source and identifier value to get curated nomenclature.

Instructions

Reverse identifier mapping: find the HGNC gene(s) for an external database id. source is the database (entrez_id/ncbi, ensembl_gene_id, uniprot, refseq, omim, ucsc, vega, ccds, mgi, rgd) and value is the id (e.g. source='ensembl_gene_id', value='ENSG00000157764'). Signature: resolve_gene_by_xref(source, value, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
valueYesThe external identifier value to look up.
sourceYesCross-reference database, e.g. entrez_id, ensembl_gene_id, uniprot.
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
hintNo
_metaNo
countNo
fieldNo
valueNo
sourceNo
messageNo
resultsNo
successNo
obsoleteNo
retryableNo
candidatesNo
error_codeNo
replaced_byNo
source_labelNo
allowed_valuesNo
recovery_actionNo
Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is clear. The description adds context like 'reverse identifier mapping' and example usage, but does not disclose additional behavioral traits such as rate limits or response format beyond the output schema.

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 extremely concise at two sentences plus a signature, with no wasted words. It front-loads the core purpose and immediately follows with specific guidance on parameters and an example pattern.

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 an output schema exists, the description appropriately omits return value details. It covers the mapping direction, source database list, and parameter structure. However, it does not mention pagination or error handling, which might be relevant for completeness.

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?

The input schema has 100% coverage with descriptions for all 3 parameters. The description adds value by explaining the relationship between source and value ('source is the database... value is the id') and providing an example (source='ensembl_gene_id', value='...'). This clarifies parameter roles beyond the schema.

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 does 'reverse identifier mapping: find the HGNC gene(s) for an external database id'. It specifies the verb (find) and resource (HGNC genes), and distinguishes from sibling tools like get_gene and resolve_symbol by emphasizing cross-reference lookup. The example signature and usage further clarify the purpose.

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 explicitly states the use case: reverse mapping from external database IDs to HGNC genes. It lists possible source databases, providing context for when to use this tool. However, it does not explicitly mention alternatives or when not to use it, missing some comparative 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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