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Map Cross-Ontology

map_cross_ontology

Read-onlyIdempotent

Retrieve cross-references for an Orphanet disorder to other ontologies like OMIM, MONDO, and ICD-10, grouped by source with mapping relations. Optionally filter by specific sources.

Instructions

List an Orphanet disorder's cross-references to other ontologies, grouped by source (OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA), each with its mapping relation. Returns them under mappings (get_disease returns the same data under xrefs). Use prefixes=['OMIM'] to restrict to a subset of sources. count is the number of leaf mapping rows (individual targets), not the number of source groups. Signature: map_cross_ontology(term, prefixes=, response_mode=).

Input Schema

TableJSON Schema

Name	Required	Description	Default
`term`	Yes	An ORPHAcode (ORPHA:33069 or 33069), a disease label/synonym, or an external xref CURIE that resolves to a single Orphanet term.
`prefixes`	No	Restrict the cross-reference sources returned to this subset (any of the xref sources: OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA). Omit to return every source.
`response_mode`	No	Verbosity: minimal\|compact\|standard\|full (default compact).	compact

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedv0.4.0Jul 17, 2026

changedInput schema / properties / prefixes / anyOf

Previous value: -[
-  {
-    "items": {
-      "type": "string"
-    },
-    "type": "array"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "items": {
+      "enum": [
+        "OMIM",
+        "MONDO",
+        "ICD-10",
+        "ICD-11",
+        "UMLS",
+        "GARD",
+        "MeSH",
+        "MedDRA"
+      ],
+      "type": "string"
+    },
+    "type": "array"
+  },
+  {
+    "type": "null"
+  }
+]

changedInput schema / properties / prefixes / description

Previous value: -"Restrict to these source prefixes, e.g. ['OMIM', 'MONDO']."New value: +"Restrict the cross-reference sources returned to this subset (any of the xref sources: OMIM/MONDO/ICD-10/ICD-11/UMLS/GARD/MeSH/MedDRA). Omit to return every source."

changedInput schema / properties / term / description

Previous value: -"An ORPHAcode (ORPHA:166024 or 166024), a disease label/synonym, or an external xref CURIE that resolves to a single Orphanet term."New value: +"An ORPHAcode (ORPHA:33069 or 33069), a disease label/synonym, or an external xref CURIE that resolves to a single Orphanet term."

changedInput schema / properties / term / examples

Previous value: -[
-  "ORPHA:166024",
-  "Aicardi syndrome",
-  "OMIM:607131"
-]New value: +[
+  "ORPHA:33069",
+  "ORPHA:166024",
+  "Dravet syndrome",
+  "OMIM:607131"
+]

addedInput schema / properties / term / maxLength
```
Added value: +256
```

changedOutput schema / (root)

Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "allowed_values": {
-      "type": "array"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "count": {
-      "type": "integer"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "hint": {
-      "type": "string"
-    },
-    "mappings": {
-      "additionalProperties": {
-        "items": {
-          "additionalProperties": true,
-          "properties": {
-            "name": {
-              "type": "string"
-            },
-            "object_id": {
-              "type": "string"
-            },
-            "origin": {
-              "type": "string"
-            },
-            "predicate": {
-              "type": "string"
-            },
-            "predicates": {
-              "type": "array"
-            },
-            "source": {
-              "type": [
-                "string",
-                "null"
-              ]
-            }
-          },
-          "type": "object"
-        },
-        "type": "array"
-      },
-      "type": "object"
-    },
-    "message": {
-      "type": "string"
-    },
-    "name": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "orpha_code": {
-      "type": "string"
-    },
-    "orphanet_version": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "prefixes_filter": {
-      "type": [
-        "array",
-        "null"
-      ]
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    }
-  },
-  "type": "object"
-}New value: +null

First observedv0.1.0Jun 18, 2026

TDQS

A4.4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint. Description adds details on data structure (mappings vs xrefs), count semantics, and function signature, going beyond 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?

Two focused sentences plus signature line, front-loaded with purpose, no waste.

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?

No output schema, but description explains output grouping and field name, count nuance, and signature. Lacks mapping relation types, but still fairly 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%, baseline 3. Description adds value by clarifying prefixes usage, count meaning, and response_mode options, plus examples and signature.

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 lists cross-references to other ontologies grouped by source with mapping relations, and distinguishes from sibling get_disease which returns same data under xrefs.

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 on when to use (get cross-references), how to restrict sources (prefixes), and notes alternative get_disease for same data. Lacks explicit when-not-to-use but covers main guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Map Cross-Ontology

Instructions

Input Schema

Schema Changelog

TDQS

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