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by berntpopp
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

Resolve Gene Symbols (Batch)

resolve_symbols_batch
Read-onlyIdempotent

Resolve up to 200 gene symbols/HGNC IDs in one call via current->previous->alias cascade. Misses or obsolete entries marked unresolved; batch never fails, returns results and counts.

Instructions

Resolve a batch of gene symbols / HGNC ids in one call (max 200). Each entry is resolved with the same current->previous->alias cascade as resolve_symbol; an individual miss or withdrawal never fails the batch (it is marked unresolved / obsolete in that entry). Returns per-query results plus resolved/unresolved counts. Signature: resolve_symbols_batch(queries, 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": {
      "queries": "<queries>"
    },
    "name": "resolve_symbols_batch"
  }
}

Input Schema

NameRequiredDescriptionDefault
queriesYesGene symbols and/or HGNC ids to resolve (max 200).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv2.1.0
    • addedInput schema / properties / queries / examples
      Added value: +[
+  [
+    "BRCA1",
+    "TP53",
+    "HGNC:1100"
+  ]
+]
    • changedOutput schema / (root)
      Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "allowed_values": {
-      "type": "array"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "hint": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "obsolete": {
-      "type": "boolean"
-    },
-    "query_count": {
-      "type": "integer"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "replaced_by": {
-      "type": "array"
-    },
-    "resolved_count": {
-      "type": "integer"
-    },
-    "results": {
-      "type": "array"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "unresolved_count": {
-      "type": "integer"
-    }
-  },
-  "type": "object"
-}New value: +null
  2. First observedv1.0.2

TDQS

A4.7/5.0
Behavior5/5

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

Discloses the resolution cascade, individual miss behavior (marked unresolved/obsolete), and returned counts. No contradictions with annotations (readOnlyHint, idempotentHint, etc.).

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?

Three focused sentences with no redundancy. Front-loaded with purpose. Highly efficient.

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?

Explains return values (per-query results + counts) despite no output schema. Could briefly describe what each response_mode yields, but overall sufficiently complete for a batch read tool.

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

Parameters5/5

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

Schema has 100% coverage, but description adds significant context: explains the cascade, batch safety, and that response_mode controls verbosity. Mentions signature for clarity.

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 resolves a batch of gene symbols/HGNC IDs (max 200) with the same cascade as resolve_symbol. It specifies per-query results and counts, distinguishing it from sibling tools like resolve_symbol.

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?

Provides clear context for batch usage (max 200) and behavior on misses/withdrawals. Implicitly suggests using resolve_symbol for single queries, but lacks an explicit when-not statement.

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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