io.github.cyanheads/pubchem-mcp-server
io.github.cyanheads/pubchem-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/dd11a987-90c2-4987-a524-b0250568a62c/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/pubchem-mcp-server"
title: null
description: "Search PubChem compounds, properties, safety data, bioactivity, and cross-references."
version: "0.8.1"
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/pubchem-mcp-server"
provider: "github"
owner: "cyanheads"
name: "pubchem-mcp-server"
verified: false
packages[2]
0{4}
registry_type: "npm"
identifier: "@cyanheads/pubchem-mcp-server"
version: "0.8.1"
transport: "stdio"
1{4}
registry_type: "npm"
identifier: "@cyanheads/pubchem-mcp-server"
version: "0.8.1"
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://pubchem.caseyjhand.com/mcp"
endpoint_host: "pubchem.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[10]
0{9}
name: "pubchem_get_bioactivity"
title: "Get Bioactivity"
effect: "READ"
effect_confidence: 0.868
capabilities[1]
0{2}
capability: "PERSONAL_DATA"
confidence: 0.567
risk_severity: "LOW"
fingerprint: "0d5927ee3f92192e69ac399b7b4773a0389063616778cea412c997a68fd5c8b4"
input_schema_fingerprint: "8969ef6e77b505fca40a6a8fea903860174c1cac0a277bece887a64e1d27f24a"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
1{9}
name: "pubchem_get_compound_3d_structure"
title: "Get Compound 3D Structure"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "a06864fe69a2318d165f75aa3928b8e171a9dd4af3131139f5c84736a2de2a75"
input_schema_fingerprint: "0b3ea2ff8f74695237e9fb6f9279b59a9507d89cdcd9d87ba755f619bac612da"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
2{9}
name: "pubchem_get_compound_details"
title: "Get Compound Details"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "2337a3e47af8cb7eced491ce4ac400b01f13f0a613d17498c2e7e0ef2afadb14"
input_schema_fingerprint: "de32e60db912a6370ec2fd014294537adcc751c0c593ca3b44a76cd3d0ff4931"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
3{9}
name: "pubchem_get_compound_image"
title: "Get Compound Image"
effect: "READ"
effect_confidence: 0.868
capabilities[0]
risk_severity: "INFO"
fingerprint: "88d766ecedd5ec7abd0d215076711d31e8054d94c64e14d62f4332dccb9717e0"
input_schema_fingerprint: "8a9df33bd0912c544b0246a16874f941bef61f30e9f72b25ff16d14e5e289fd0"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
4{9}
name: "pubchem_get_compound_interactions"
title: "Get Compound Interactions"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "d4813c420fa9c5bf3ce9ddc136afa24e470cb6aa3fd930588c007b1fae0568f7"
input_schema_fingerprint: "3b52f6553a74b1f272757ebcd951818625666d17112a32b513c54a47b3e24a9e"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
5{9}
name: "pubchem_get_compound_safety"
title: "Get Compound Safety"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "617539ed9b3c74bebb1f8c44531f7befb08256f24ea82bcd5e68c465870eaf4d"
input_schema_fingerprint: "f0bdf5c9ca6508854097ed8de9f1d5ed2b934f5847392220b7f180441ca49231"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
6{9}
name: "pubchem_get_compound_xrefs"
title: "Get Compound Cross-References"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "328b328f6e76d4a40996d4d2dd2766f015bbac3280c7a72fe63032b80e64ff80"
input_schema_fingerprint: "81ccb496a27d13c451677812e1f03408404badebe7dd66eaa78aed7c743be967"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
7{9}
name: "pubchem_get_summary"
title: "Get Entity Summary"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "2a973062a90a0895c19cd6a0736aec49a357495a678cf3c6367d2a614fb92494"
input_schema_fingerprint: "885060a19eefbbd8e1e25568dfd8f40997bab37fb45f883a517b90897cca28f9"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
8{9}
name: "pubchem_search_assays"
title: "Search Assays"
effect: "READ"
effect_confidence: 0.888
capabilities[0]
risk_severity: "INFO"
fingerprint: "70810404caa3c39603740a3301679cf22907c4315fbc3ef5e85c01efc32f22b5"
input_schema_fingerprint: "31a4fae01f503bf0e3cb34bdb69d6f99327c35793b2969f959a0be22c066b5b6"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
9{9}
name: "pubchem_search_compounds"
title: "Search Compounds"
effect: "READ"
effect_confidence: 0.905
capabilities[0]
risk_severity: "INFO"
fingerprint: "925fbbd336381e03699bbb1d724ebcce923de52f0449168d08caab619f9ca4aa"
input_schema_fingerprint: "221b3fc309e88ae34cdeb2b35c37dfcb2d44bf08cf34b010c2e8e5d7854dceeb"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: true
openWorldHint: true
resources[8]
0{4}
key: "skill://pubchem-guide/SKILL.md"
kind: "resource"
mime_type: "text/markdown"
fingerprint: "7693c720f479b3f3f12098b4853f305a9e076f2163af8bc509ed09d76bf0e403"
1{4}
key: "pubchem://assay/{aid}"
kind: "template"
mime_type: "application/json"
fingerprint: "e263b2c69e781dacee844f38c358a60d6a67c8ceb65417ae9cb4a26c0e3c313d"
2{4}
key: "pubchem://compound/{cid}"
kind: "template"
mime_type: "application/json"
fingerprint: "5f8265aa5c92878e6ba6fbc7f4762a6f9cdb736d31c42eeb593646d55a797293"
3{4}
key: "pubchem://compound/{cid}/bioactivity"
kind: "template"
mime_type: "application/json"
fingerprint: "6991e0281a5ce39f8def395f5265e3c7047a80c7f2c3767d4a8b7df7feb0b74f"
4{4}
key: "pubchem://compound/{cid}/image"
kind: "template"
mime_type: "image/png"
fingerprint: "4a3b3c4f31e658d61a39e8fcb76bf417fe33405aab1822edf1ed03436bb2aad5"
5{4}
key: "pubchem://compound/{cid}/safety"
kind: "template"
mime_type: "application/json"
fingerprint: "5ee7d08a144a41b34f427966b588dcce6e1da6de51a9baab7203df8a33b8303c"
6{4}
key: "pubchem://compound/{cid}/xrefs"
kind: "template"
mime_type: "application/json"
fingerprint: "81b05f8dacd55927c71516b9cddf532d5e5b339642832918dca25f7d6b09c64f"
7{4}
key: "skill://{+path}"
kind: "template"
mime_type: null
fingerprint: "9777dc7f1cf468158c157032a0ccebf9b50270f4e8753af9ccaf2fe99890ccf0"
prompts[0]
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: "pubchem.caseyjhand.com"
registrable_domain: "caseyjhand.com"
source: "transport"
findings[5]
0{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: "pubchem_get_bioactivity"
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: "pubchem_get_compound_details"
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: "pubchem_get_compound_xrefs"
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: "pubchem_search_assays"
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: "pubchem_search_compounds"
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/pubchem-mcp-server"
registry_content_sha256: "f04b3952ba3717e0c75fe7682642a060386b82045de9cf545bcfcacb8fd631a7"
scan_snapshot_fingerprint: "93d632b4ae55c4051ba623c4461b91a00e93829c0ac901425c76ee66f0388ccd"
scanner_version: "1.0.0"
timestamps{4}
generated_at: "2026-11-15T02:14:34.904Z"
observed_at: "2026-11-11T12:23:55.978+00:00"
registry_published_at: "2026-11-11T07:33:23.858623+00:00"
registry_updated_at: null