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Folklore Clinical Variant Interpretation MCP

by io.github.helena-bioinformatics
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Find diseases associated with a gene

get_gene_disease_associations
Read-onlyIdempotent

Find diseases associated with an exact gene symbol or HGNC identifier. Returns ClinGen gene-disease validity assertions, relation-specific inheritance, source reports and snapshot provenance, including conflicting and limited assertions.

Input Schema

NameRequiredDescriptionDefault
geneYesOne public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100.
limitNoMaximum number of source assertions per page, from 1 to 50.
offsetNoZero-based assertion offset; use the returned nextOffset when present.

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed7 schema fields changed
    • changedInput schema / properties / gene / description
      Previous value: -"One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data."New value: +"One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100."
    • removedOutput schema / $defs / UsageBoundary
      Removed value: -{
-  "additionalProperties": false,
-  "properties": {
-    "intended_use": {
-      "const": "professional_gene_disease_review",
-      "title": "Intended Use",
-      "type": "string"
-    },
-    "not_for": {
-      "items": {
-        "enum": [
-          "patient_diagnosis",
-          "treatment_decision",
-          "variant_pathogenicity_classification"
-        ],
-        "type": "string"
-      },
-      "title": "Not For",
-      "type": "array"
-    },
-    "patient_context_evaluated": {
-      "const": false,
-      "title": "Patient Context Evaluated",
-      "type": "boolean"
-    },
-    "review_required": {
-      "const": true,
-      "title": "Review Required",
-      "type": "boolean"
-    }
-  },
-  "required": [
-    "intended_use",
-    "patient_context_evaluated",
-    "review_required",
-    "not_for"
-  ],
-  "title": "UsageBoundary",
-  "type": "object"
-}
    • removedOutput schema / additionalProperties
      Removed value: -false
    • addedOutput schema / anyOf
      Added value: +[
+  {
+    "additionalProperties": false,
+    "properties": {
+      "associations": {
+        "items": {
+          "$ref": "#/$defs/Association"
+        },
+        "maxItems": 50,
+        "title": "Associations",
+        "type": "array"
+      },
+      "contractVersion": {
+        "const": "2",
+        "title": "Contractversion",
+        "type": "string"
+      },
+      "pagination": {
+        "$ref": "#/$defs/Pagination"
+      },
+      "query": {
+        "$ref": "#/$defs/Query"
+      },
+      "source": {
+        "$ref": "#/$defs/Source"
+      },
+      "status": {
+        "enum": [
+          "ok",
+          "not_found"
+        ],
+        "title": "Status",
+        "type": "string"
+      },
+      "warnings": {
+        "items": {
+          "type": "string"
+        },
+        "title": "Warnings",
+        "type": "array"
+      }
+    },
+    "required": [
+      "contractVersion",
+      "status",
+      "query",
+      "associations",
+      "pagination",
+      "source",
+      "warnings"
+    ],
+    "title": "GeneDiseaseResponse",
+    "type": "object"
+  },
+  {
+    "additionalProperties": false,
+    "properties": {
+      "adapter_error": {
+        "additionalProperties": false,
+        "properties": {
+          "code": {
+            "type": "string"
+          },
+          "message": {
+            "type": "string"
+          },
+          "retryable": {
+            "type": "boolean"
+          }
+        },
+        "required": [
+          "code",
+          "message",
+          "retryable"
+        ],
+        "type": "object"
+      },
+      "contractVersion": {
+        "const": "2"
+      }
+    },
+    "required": [
+      "contractVersion",
+      "adapter_error"
+    ],
+    "type": "object"
+  }
+]
    • removedOutput schema / properties
      Removed value: -{
-  "associations": {
-    "items": {
-      "$ref": "#/$defs/Association"
-    },
-    "maxItems": 50,
-    "title": "Associations",
-    "type": "array"
-  },
-  "contractVersion": {
-    "const": "1.0",
-    "title": "Contractversion",
-    "type": "string"
-  },
-  "pagination": {
-    "$ref": "#/$defs/Pagination"
-  },
-  "query": {
-    "$ref": "#/$defs/Query"
-  },
-  "source": {
-    "$ref": "#/$defs/Source"
-  },
-  "status": {
-    "enum": [
-      "ok",
-      "not_found"
-    ],
-    "title": "Status",
-    "type": "string"
-  },
-  "usage_boundary": {
-    "$ref": "#/$defs/UsageBoundary"
-  },
-  "warnings": {
-    "items": {
-      "type": "string"
-    },
-    "title": "Warnings",
-    "type": "array"
-  }
-}
    • removedOutput schema / required
      Removed value: -[
-  "contractVersion",
-  "status",
-  "query",
-  "associations",
-  "pagination",
-  "source",
-  "warnings",
-  "usage_boundary"
-]
    • removedOutput schema / title
      Removed value: -"GeneDiseaseResponse"
  2. Added

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, closed-world, non-destructive, so the safety profile is covered. The description adds real context beyond that: what the payload contains (ClinGen gene-disease validity assertions, relation-specific inheritance, source reports, snapshot provenance) and that conflicting and limited assertions are included, which tells the agent to expect low-confidence results rather than treat them as errors.

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 tight sentences: the first front-loads the action and accepted inputs, the second enumerates the returned content. No filler, no restatement of the title or annotations.

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?

With an output schema present and full parameter descriptions, the description need only frame the tool's role, which it does. The main remaining gap is the lack of explicit routing guidance to resolve_gene or to the gene-profile siblings for agents holding an ambiguous gene name.

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

Parameters3/5

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

Schema coverage is 100%, so gene, limit, and offset are already fully documented with examples and bounds. The description reinforces the exact-match requirement on the gene argument but adds no meaning for the pagination parameters, so the baseline 3 applies.

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?

States a specific verb and resource ('Find diseases associated with a gene') plus the accepted identifier forms, so the agent knows exactly what is being looked up. It does not distinguish itself from nearby siblings such as get_gene_profile, get_gene_section, or search_disease_genes, so it stops just short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is implied by the 'exact gene symbol or HGNC identifier' phrasing, which hints that an unresolved name must be normalized first, but no alternative tool (e.g., resolve_gene) is named and there are no explicit when-not conditions. Adequate but leaves routing to inference.

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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