io.github.cyanheads/ensembl-mcp-server
io.github.cyanheads/ensembl-mcp-server
MCP Bill of Materials
A machine-readable inventory of what this server exposes and depends on: tools with their effects, transports, packages, findings and provenance (schema version 1.0). Third-party text in it is escaped. Also available from the REST API at /api/v1/servers/bf23ec17-acd6-4776-b125-f922b694e20c/mcbom.
MCP Bill of Materials
root{21}
schema_version: "1.0"
bom_format: "squatch-mcbom"
generator{3}
name: "squatch-mcp"
classifier_version: "rules_v1@2026-10-11.1"
unicode_version: "18.0.0"
server{7}
name: "io.github.cyanheads/ensembl-mcp-server"
title: null
description: "Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST."
version: "0.7.1"
homepage_url: null
source: "official_registry"
upstream_status: "active"
publisher{4}
namespace: "io.github.cyanheads"
display_name: "io.github.cyanheads"
type: "registry_namespace"
status: "unclaimed"
organization: null
repository{5}
url: "https://github.com/cyanheads/ensembl-mcp-server"
provider: "github"
owner: "cyanheads"
name: "ensembl-mcp-server"
verified: false
packages[2]
0{4}
registry_type: "npm"
identifier: "@cyanheads/ensembl-mcp-server"
version: "0.7.1"
transport: "stdio"
1{4}
registry_type: "npm"
identifier: "@cyanheads/ensembl-mcp-server"
version: "0.7.1"
transport: "streamable-http"
transports[3]
0{5}
kind: "package"
type: "stdio"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
1{5}
kind: "package"
type: "streamable-http"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
2{5}
kind: "remote"
type: "streamable-http"
endpoint_url: "https://ensembl.caseyjhand.com/mcp"
endpoint_host: "ensembl.caseyjhand.com"
auth_type: "none"
auth{3}
type: "none"
authorization_servers[0]
scopes[0]
protocol{4}
era: "modern"
negotiated_version: "2026-07-28"
supported_versions[0]
transport_type: "streamable-http"
tools[7]
0{9}
name: "ensembl_get_homology"
title: "Get Gene Homologs"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "f1dea138f2d4ae67cf32fb7df07eb764eb9eb5dc70f04bb5acaac8aa9801471b"
input_schema_fingerprint: "c3eb0a1a14496e6c8ea6ba5c9aca1ff88b55e2fb3ca56b70b2361d3f685e9caa"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
1{9}
name: "ensembl_get_sequence"
title: "Get Sequence"
effect: "READ"
effect_confidence: 0.888
capabilities[1]
0{2}
capability: "SENSITIVE_PERSONAL_DATA"
confidence: 0.632
risk_severity: "MEDIUM"
fingerprint: "bc2d22e6e7f6ed4077bedf5fffe8b4963827754a323b9f17b47d005eb9c73163"
input_schema_fingerprint: "b80517e2ad91e5c025d641ce015a8c384d80d4a054755647df1090a37ae25749"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
2{9}
name: "ensembl_get_xrefs"
title: "Get Cross-Database References"
effect: "READ"
effect_confidence: 0.888
capabilities[1]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.853
risk_severity: "INFO"
fingerprint: "25ea02c9cbc297eca15bca66318a25bad4fa84066d7336800f39a0e7ed8af5e4"
input_schema_fingerprint: "137d68ac168b2a3b7b38b89238ee7b855e833dcb4945a4dbf43d35cb4f679bbc"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
3{9}
name: "ensembl_list_species"
title: "List Ensembl Species"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "8c39a5c578b7233b729cfd3b2a4edb156ad2cd4ed350098675b99c18a5baf173"
input_schema_fingerprint: "b3d36727541193f59a58c55140a90f9f3f5ca12b1c86264bb95d268872810d8d"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
4{9}
name: "ensembl_lookup_gene"
title: "Lookup Gene"
effect: "READ"
effect_confidence: 0.905
capabilities[1]
0{2}
capability: "PERSONAL_DATA"
confidence: 0.897
risk_severity: "LOW"
fingerprint: "f5d95a3f7a4d457ab6f8de050834ec16c3ad77471f5d288748d2ee56a0eae33b"
input_schema_fingerprint: "84661bf99f2c7bda64837be01ec4ee68efd3326eb81ef8bb63f11c524ccf6094"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
5{9}
name: "ensembl_predict_variant"
title: "Predict Variant Effect"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "13ec1093dd394f468b9dd468fc50c7f098f05aac17c33a18b071c540da9801b6"
input_schema_fingerprint: "0cd83b883b8406ac0fd43e5713dafb1eed4413de70a86a8f57e508b714faa597"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
6{9}
name: "ensembl_query_region"
title: "Query Genomic Region"
effect: "READ"
effect_confidence: 0.776
capabilities[1]
0{2}
capability: "CLOUD_INFRASTRUCTURE"
confidence: 0.669
risk_severity: "INFO"
fingerprint: "12bbd71396f6eb417ad5f4de53419ae1126fe8ba21e3c1ee14a9f9438a3e1150"
input_schema_fingerprint: "100a1fe2ce9fd6db5af60ab449ce6fca051f4f862f496484fddcdbba8ef91a4e"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
resources[14]
0{4}
key: "ensembl://gene/ENSG00000139618"
kind: "resource"
mime_type: "application/json"
fingerprint: "ac8dd9a4c7d8267bc9d27e7155cfe1233bfa2df85451e3012608e063701de00c"
1{4}
key: "ensembl://gene/ENSG00000141510"
kind: "resource"
mime_type: "application/json"
fingerprint: "46f3dd7c168bac9ab485d0eb756340f9a9a570574e3ef98fbf88fced253d9891"
2{4}
key: "ensembl://species"
kind: "resource"
mime_type: "application/json"
fingerprint: "1abc754b7b0da91ef96700bad1231a9c2efd43de4483e2bdf981cafb200e298f"
3{4}
key: "ensembl://species/EnsemblFungi"
kind: "resource"
mime_type: "application/json"
fingerprint: "8966f7a04f0b79a76033f413d866ae0e77d114dd30dfc02e73f9873c6fce0254"
4{4}
key: "ensembl://species/EnsemblMetazoa"
kind: "resource"
mime_type: "application/json"
fingerprint: "c9ecf77531fe55e7a1759f7b4bea51a532d2fdc510139bd3505d7cc86cda2cfd"
5{4}
key: "ensembl://species/EnsemblPlants"
kind: "resource"
mime_type: "application/json"
fingerprint: "cbd8db4109622a5fe0233531b25d3f7e39028fdb7b3f8e9ca2069038ccdb02ed"
6{4}
key: "ensembl://species/EnsemblProtists"
kind: "resource"
mime_type: "application/json"
fingerprint: "ad520e933417189567dcff774d4885283921751de34a4b45ca50ce58d671904b"
7{4}
key: "ensembl://species/EnsemblVertebrates"
kind: "resource"
mime_type: "application/json"
fingerprint: "60ac8396fcc538ba4bfd29f519eea9b1b5a8e8ed70558dac0f6e1805216cce61"
8{4}
key: "ensembl://transcript/ENST00000380152"
kind: "resource"
mime_type: "application/json"
fingerprint: "6f080fee21f3439ac8a5f3ed641f9eef7a7d04aaef63d3f5ae2c28bf46156319"
9{4}
key: "skill://ensembl-guide/SKILL.md"
kind: "resource"
mime_type: "text/markdown"
fingerprint: "c4367024e33b5627002b79ec8300492d2c3c43aa47b8fb097b80205e170f602b"
10{4}
key: "ensembl://gene/{id}"
kind: "template"
mime_type: "application/json"
fingerprint: "2c25f936854ae46636e69d846c0381f67398f40a424ee27a20fe20a5b497a52f"
11{4}
key: "ensembl://species/{division}"
kind: "template"
mime_type: "application/json"
fingerprint: "4856f4aa8ccef0f2e3e48fb5ac184eaa4c11443f8e7120e77ce508e81fb0d680"
12{4}
key: "ensembl://transcript/{id}"
kind: "template"
mime_type: "application/json"
fingerprint: "a797db252725bff752c99a20b85fbbeca5aad8ab965a8ce3bf64f1e2a9242d01"
13{4}
key: "skill://{+path}"
kind: "template"
mime_type: null
fingerprint: "9777dc7f1cf468158c157032a0ccebf9b50270f4e8753af9ccaf2fe99890ccf0"
prompts[1]
0{2}
name: "ensembl_gene_dossier"
fingerprint: "9f9291e6f44d13bc311db3b03b646d1df8b89758e04b79f056498f30dc33f032"
extensions[1]
0: "io.modelcontextprotocol/skills"
data{6}
privacy_completeness: "not_provided"
data_categories[0]
ai_training: null
retention_policy: null
processing_regions[0]
subprocessors[0]
external_integrations[1]
0{3}
host: "ensembl.caseyjhand.com"
registrable_domain: "caseyjhand.com"
source: "transport"
findings[6]
0{6}
check_id: "SQ-RESOURCE-INJECTION"
category: "prompt_injection"
severity: "HIGH"
title: "Resource metadata contains directives to the AI model"
subject_type: "server"
subject_name: null
1{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "ensembl_list_species"
2{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "ensembl_lookup_gene"
3{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "ensembl_predict_variant"
4{6}
check_id: "SQ-TOOL-EXFIL-DIRECTIVE"
category: "prompt_injection"
severity: "HIGH"
title: "Asks the AI model to pass conversation data or secrets"
subject_type: "tool"
subject_name: "ensembl_query_region"
5{6}
check_id: "SQ-TOOL-INJECTION-INSTRUCTIONS"
category: "prompt_injection"
severity: "MEDIUM"
title: "Instructions addressed to the AI model"
subject_type: "tool"
subject_name: "ensembl_query_region"
trust{9}
registry_namespace: "verified_upstream"
publisher_identity: "unverified"
organization: "unverified"
domain: "unverified"
repository: "unverified"
source_provenance: "partial"
security_scan: "findings_detected"
privacy_transparency: "not_provided"
monitoring: "active"
provenance{4}
registry_name: "io.github.cyanheads/ensembl-mcp-server"
registry_content_sha256: "0c6f850412028fcc94d072f934277a6faa0fd715f64473e837d32995e8670fd3"
scan_snapshot_fingerprint: "d46f23ea2c8fd1aef78d5e9007c090599700c0ddea8c4d04881df6c7cb14bbd8"
scanner_version: "1.0.0"
timestamps{4}
generated_at: "2026-11-15T02:14:28.305Z"
observed_at: "2026-11-08T16:28:54.669+00:00"
registry_published_at: "2026-10-29T10:48:33.448559+00:00"
registry_updated_at: null