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gencc-link

by berntpopp
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Python
Remote

Resolve Identifier

resolve_identifier
Read-onlyIdempotent

Resolve free-text queries to canonical gene or disease identifiers using exact matches. Specify kind to disambiguate between gene and disease, or use auto mode to detect ambiguous queries.

Instructions

Resolve free text to a canonical GenCC gene (HGNC) and/or disease (MONDO) identifier by exact symbol/id/title match. Use kind='gene' or kind='disease' to disambiguate; default 'auto' tries both and returns ambiguous_query if the text matches both a gene and a disease.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
kindNoResolution scope: auto (both), gene, or disease.auto
queryYesFree text to resolve: a gene symbol, HGNC id, disease title, or MONDO/OMIM id.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed11 schema fields changedv0.8.2
    • removedInput schema / properties / identifier
      Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null
-}
    • addedInput schema / properties / kind / description
      Added value: +"Resolution scope: auto (both), gene, or disease."
    • addedInput schema / properties / kind / enum
      Added value: +[
+  "auto",
+  "gene",
+  "disease"
+]
    • addedInput schema / properties / kind / examples
      Added value: +[
+  "auto"
+]
    • removedInput schema / properties / query / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
    • removedInput schema / properties / query / default
      Removed value: -null
    • addedInput schema / properties / query / description
      Added value: +"Free text to resolve: a gene symbol, HGNC id, disease title, or MONDO/OMIM id."
    • addedInput schema / properties / query / examples
      Added value: +[
+  "BRCA1",
+  "Noonan syndrome"
+]
    • addedInput schema / properties / query / type
      Added value: +"string"
    • addedInput schema / required
      Added value: +[
+  "query"
+]
    • changedOutput schema / (root)
      Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "description": "Per-call envelope metadata.",
-      "properties": {
-        "citation_ref": {
-          "type": "string"
-        },
-        "citation_short": {
-          "type": "string"
-        },
-        "data_license": {
-          "type": "string"
-        },
-        "elapsed_ms": {
-          "type": "number"
-        },
-        "gencc_release": {
-          "type": "string"
-        },
-        "next_commands": {
-          "items": {
-            "additionalProperties": false,
-            "properties": {
-              "arguments": {
-                "additionalProperties": true,
-                "type": "object"
-              },
-              "tool": {
-                "type": "string"
-              }
-            },
-            "required": [
-              "tool",
-              "arguments"
-            ],
-            "type": "object"
-          },
-          "type": "array"
-        },
-        "recommended_citation": {
-          "type": "string"
-        },
-        "request_id": {
-          "type": "string"
-        },
-        "response_mode": {
-          "type": "string"
-        },
-        "tool": {
-          "type": "string"
-        },
-        "unsafe_for_clinical_use": {
-          "type": "boolean"
-        }
-      },
-      "type": "object"
-    },
-    "disease": {
-      "additionalProperties": true,
-      "type": [
-        "object",
-        "null"
-      ]
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field_errors": {
-      "items": {
-        "additionalProperties": true,
-        "type": "object"
-      },
-      "type": "array"
-    },
-    "gene": {
-      "additionalProperties": true,
-      "type": [
-        "object",
-        "null"
-      ]
-    },
-    "headline": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "query": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    }
-  },
-  "required": [
-    "success"
-  ],
-  "type": "object"
-}New value: +null
  2. First observedv0.5.3

TDQS

A4.4/5.0
Behavior4/5

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

Annotations already establish read-only, idempotent, non-destructive behavior. The description adds meaningful behavioral details: exact match criterion, canonical identifier types, and the ambiguous_query return condition. It does not cover no-match behavior, but the provided context goes beyond the annotations.

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 long, front-loaded with the core purpose, and contains no redundant wording. Every sentence contributes useful information.

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?

The description covers purpose, matching semantics, disambiguation, and a special return case. Minor gaps include no-match behavior and explicit return format, but given the simplicity of the tool and absence of an output schema, it is largely complete.

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% with both parameters well-described. The description reinforces query content and explains the effect of kind, including the ambiguous_query outcome, adding semantic value beyond the schema's basic parameter 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's function: resolving free text to canonical GenCC gene (HGNC) and/or disease (MONDO) identifiers via exact match. This distinguishes it from sibling search tools by emphasizing canonical identifier resolution rather than general search.

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 provides explicit guidance on using kind='gene' or kind='disease' to disambiguate, and explains the default 'auto' behavior with ambiguous_query. While it doesn't name alternative tools, the usage context for this resolver is clear and actionable.

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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