ensembl-mcp-server

Get Cross-Database References

ensembl_get_xrefs

Read-onlyIdempotent

Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description. The dbname filter narrows to specific databases; omit to return all xrefs. IDs returned here chain to protein (pubchem via UniProt), literature (pubmed via PubMed IDs), disease (OMIM via MIM_GENE), and pathway (Reactome) resources. Requires an Ensembl stable ID — use ensembl_lookup_gene to get the ENSG… ID first. Common dbname values: HGNC, Uniprot_gn, EntrezGene, MIM_GENE, RefSeq_mRNA, RefSeq_peptide, Reactome, GO (Gene Ontology), ChEMBL.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`id`	Yes	Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2).
`dbname`	No	Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome (pathway IDs), GO (Gene Ontology terms). Omit to return all available xrefs.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`xrefs`	No	Cross-database references for the queried Ensembl ID.
`notice`	No	Guidance when no cross-references are found.
`queriedId`	No	The Ensembl stable ID that was queried.
`totalCount`	No	Total number of cross-references returned.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedSep 24, 2026
- addedInput schema / properties / id / minLength
```
Added value: +1
```

Changed6 schema fields changedAug 22, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedInput schema / additionalProperties
```
Added value: +false
```

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "xrefs",
+      "totalCount",
+      "queriedId"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `not_found`: The Ensembl stable ID was not found or has no cross-references. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "not_found"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

removedOutput schema / required

Removed value: -[
-  "xrefs",
-  "totalCount",
-  "queriedId"
-]

First observedJun 7, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and openWorldHint=true, so the safety profile is covered. The description adds useful behavioral context: it requires an Ensembl stable ID, explains that the returned IDs chain to other resources (protein, literature, disease, pathway), and notes that well-annotated genes return 56+ entries. It doesn't contradict annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single dense paragraph that front-loads the core purpose and then adds usage details. It's slightly long but every sentence earns its place: purpose, return contents, filter behavior, chaining semantics, prerequisite, and common values. The structure could be improved with bullet points, but it's not bloated.

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?

Given the tool's moderate complexity, the description covers the prerequisite, the filter behavior, the return contents, and the chaining semantics. The output schema exists, so return values don't need to be re-explained. The only minor gap is that it doesn't explicitly state what happens when an invalid ID is provided, but that's a minor omission for a read-only lookup tool.

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 description coverage is 100%, so the schema already documents both parameters thoroughly. The description adds some value by listing common dbname values and explaining the chaining semantics of returned IDs, but it doesn't go beyond the schema's parameter descriptions in a major way. Baseline 3 is appropriate.

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 states a specific verb ('Retrieve') and resource ('cross-database references for a gene or feature'), and enumerates the databases involved. It clearly distinguishes this from sibling tools like ensembl_get_homology or ensembl_get_sequence by focusing on xrefs and even names the sibling ensembl_lookup_gene as a prerequisite.

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

Usage Guidelines5/5

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

The description explicitly says when to use this tool: after obtaining an Ensembl stable ID via ensembl_lookup_gene, and it explains the dbname filter behavior ('narrow to specific databases; omit to return all xrefs'). It also provides common dbname values, which is actionable guidance for an agent deciding whether to call this tool.

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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