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hgnc-link

hgnc-link

by berntpopp
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

Get Gene Record

get_gene
Read-onlyIdempotent

Resolve a gene symbol, alias, previous symbol, or HGNC ID to its canonical HGNC record, with full details including name, status, locus, aliases, and cross-references.

Instructions

Return the full HGNC record for a gene, resolved from an HGNC id, current symbol, previous symbol, or alias. Includes name, status, locus group/type, location, aliases/previous symbols, gene groups, and all cross-references. response_mode controls verbosity (compact drops dates/provenance; minimal keeps identity + anchor ids). Signature: get_gene(query, response_mode=).

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": {
      "query": "<query>"
    },
    "name": "get_gene"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesA gene symbol (current/previous/alias, case-insensitive) or HGNC id (HGNC:1100 or 1100).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv2.1.0
    • changedOutput schema / (root)
      Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "alias_symbol": {
-      "type": "array"
-    },
-    "allowed_values": {
-      "type": "array"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "ensembl_gene_id": {
-      "type": "string"
-    },
-    "entrez_id": {
-      "type": "string"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "gene_group": {
-      "type": "array"
-    },
-    "gene_group_id": {
-      "type": "array"
-    },
-    "hgnc_id": {
-      "type": "string"
-    },
-    "hint": {
-      "type": "string"
-    },
-    "location": {
-      "type": "string"
-    },
-    "locus_group": {
-      "type": "string"
-    },
-    "locus_type": {
-      "type": "string"
-    },
-    "mane_select": {
-      "type": "array"
-    },
-    "match_type": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "name": {
-      "type": "string"
-    },
-    "obsolete": {
-      "type": "boolean"
-    },
-    "omim_id": {
-      "type": "array"
-    },
-    "prev_symbol": {
-      "type": "array"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "refseq_accession": {
-      "type": "array"
-    },
-    "replaced_by": {
-      "type": "array"
-    },
-    "requested_query": {
-      "type": "string"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "status": {
-      "type": "string"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "symbol": {
-      "type": "string"
-    },
-    "uniprot_ids": {
-      "type": "array"
-    }
-  },
-  "type": "object"
-}New value: +null
  2. First observedv1.0.2

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare read-only, open-world, idempotent, non-destructive. Description adds specifics: lists returned fields, explains response_mode effect (compact drops dates/provenance, minimal keeps identity+anchor ids). No contradictions.

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?

Two sentences: first describes purpose and data, second gives signature. No unnecessary words, front-loaded with key info.

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?

With 2 params fully described in schema and annotations, description covers return contents and response_mode variations. No output schema needed because description lists fields explicitly. Completeness excellent.

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 covers both parameters with descriptions and examples. Description goes beyond schema by explaining that response_mode controls verbosity with concrete examples (compact drops dates/provenance, minimal keeps identity+anchor ids).

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?

Description clearly states it returns the full HGNC record for a gene, specifies input types (HGNC id, symbol, alias), and lists contents (name, status, location, cross-refs). Distinguishes from siblings like resolve_symbol and search_genes.

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?

Describes when to use (get full record by various identifiers) and mentions response_mode verbosity levels. Lacks explicit when-not-to-use or comparison to all siblings, but context of sibling tools makes it clear.

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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