io.github.cyanheads/pubmed-mcp-server
io.github.cyanheads/pubmed-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/5e9a3605-f104-4935-90c1-56ee0779f4d6/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/pubmed-mcp-server"
title: null
description: "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms."
version: "2.12.2"
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/pubmed-mcp-server"
provider: "github"
owner: "cyanheads"
name: "pubmed-mcp-server"
verified: false
packages[2]
0{4}
registry_type: "npm"
identifier: "@cyanheads/pubmed-mcp-server"
version: "2.12.2"
transport: "stdio"
1{4}
registry_type: "npm"
identifier: "@cyanheads/pubmed-mcp-server"
version: "2.12.2"
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://pubmed.caseyjhand.com/mcp"
endpoint_host: "pubmed.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[12]
0{9}
name: "pubmed_convert_ids"
title: "Pubmed Convert Ids"
effect: "READ"
effect_confidence: 0.626
capabilities[0]
risk_severity: "INFO"
fingerprint: "c855c90af9a490f52d1ba17e3100510abf431ece4f5e0cecfd4d0ddadb31f219"
input_schema_fingerprint: "473ad3fc98c760ed5a1cad9a44e0aff8f3141f2c4816ced15306dc55a4f52778"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
1{9}
name: "pubmed_europepmc_fetch"
title: "Pubmed Europepmc Fetch"
effect: "READ"
effect_confidence: 0.813
capabilities[0]
risk_severity: "INFO"
fingerprint: "efb6e26f68429b16c028b0c19e4b0e72846866166db8f2966d3c3992f308438c"
input_schema_fingerprint: "a8cc87d5b93ff79dce2f67b4ff7177705fa796255ccce67ca33204704b143f92"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
2{9}
name: "pubmed_europepmc_search"
title: "Pubmed Europepmc Search"
effect: "READ"
effect_confidence: 0.813
capabilities[0]
risk_severity: "INFO"
fingerprint: "1e8923f469f0ef297eddb8b17557446d2f56bfacb2081cad67903ab0d023d45a"
input_schema_fingerprint: "9849586ca68400e4257f8641a22ea58fe8d26c0a569c59880dc534c732574fbb"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
3{9}
name: "pubmed_fetch_articles"
title: "Pubmed Fetch Articles"
effect: "READ"
effect_confidence: 0.813
capabilities[1]
0{2}
capability: "PERSONAL_DATA"
confidence: 0.848
risk_severity: "LOW"
fingerprint: "60128f789ad3033bb4da06ef8c64704b26c5b3c3564174d37b6542cd98ce269b"
input_schema_fingerprint: "19aec47644e9465c91a924bb4cfc5a05c3c819711bb455b22f55c6d5a05fed75"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
4{9}
name: "pubmed_fetch_citation_metrics"
title: "Pubmed Fetch Citation Metrics"
effect: "READ"
effect_confidence: 0.813
capabilities[0]
risk_severity: "INFO"
fingerprint: "a93de38c0091e96cff2812cc5ae2b1a0bd0a4bfefb1b1ea6492b5cbd8f73af57"
input_schema_fingerprint: "d7bc36982440e06c5db1a346eefb9f7012021f1640fa03206640c3e33f45b121"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
5{9}
name: "pubmed_fetch_fulltext"
title: "Pubmed Fetch Fulltext"
effect: "READ"
effect_confidence: 0.813
capabilities[0]
risk_severity: "INFO"
fingerprint: "6b2458ec5154b29e01e3edc5aee52786beb4462da7ba3e8025d84b85f4d5538c"
input_schema_fingerprint: "eca381ec62be9e174a482ef3835981b258f504a3e376e654900e988a0249ee37"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
6{9}
name: "pubmed_find_related"
title: "Pubmed Find Related"
effect: "READ"
effect_confidence: 0.78
capabilities[0]
risk_severity: "INFO"
fingerprint: "103aa5418149ad9aa390e2d3d42d582c5759aca7a2a54b38f433a65febc0f344"
input_schema_fingerprint: "01aee3d2de9af92f1cebad7e3767a011e8949c07c8001a69d6c01eef8e371658"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
7{9}
name: "pubmed_format_citations"
title: "Pubmed Format Citations"
effect: "READ"
effect_confidence: 0.626
capabilities[0]
risk_severity: "INFO"
fingerprint: "9b4f2028f2dce496682059f32326dd1e66090c18c7e2e1cf8eeb6e7b0584d05e"
input_schema_fingerprint: "c7d3b307a491dc6e3557bd4eb5f9fcd9adbcc1d46c6d74598cd49824a5a03435"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
8{9}
name: "pubmed_lookup_citation"
title: "Pubmed Lookup Citation"
effect: "READ"
effect_confidence: 0.813
capabilities[0]
risk_severity: "INFO"
fingerprint: "3b781623d9c96ae931ed308ade5ba8790cc8c691d56ce6391046caa998889842"
input_schema_fingerprint: "addf74d371d7e1335ee4f4cf435a3f8c71560b058a6546f8f915596349adafcc"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
9{9}
name: "pubmed_lookup_mesh"
title: "Pubmed Lookup Mesh"
effect: "READ"
effect_confidence: 0.841
capabilities[0]
risk_severity: "INFO"
fingerprint: "0aee278d52c7c76fa15e26c560db2a76505e876060659b99cbf5b46d77bb870d"
input_schema_fingerprint: "4c117876a267344bde575585e7bd9b8cb567d74d12bddb4c0c7c9c792a9ee36d"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
10{9}
name: "pubmed_search_articles"
title: "Pubmed Search Articles"
effect: "EXECUTE"
effect_confidence: 0.66
capabilities[1]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.624
risk_severity: "CRITICAL"
fingerprint: "2ff58053156ee8c64bda2863b00b26017e24152d7715b5b4d329d0267f83b782"
input_schema_fingerprint: "42fac1841feea85702cf49b8c2fc2778385545f368bb8cae03989b5da58a73a1"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
11{9}
name: "pubmed_spell_check"
title: "Pubmed Spell Check"
effect: "READ"
effect_confidence: 0.595
capabilities[0]
risk_severity: "INFO"
fingerprint: "596bb1cb2ba1178d2939d57dedcf1267a3625ca986bd19a141a6b5ed836d60c8"
input_schema_fingerprint: "19d31d8b3cbdd845cded4be9fc540500bc169cc9a8ccf804372de8b46c13a922"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
resources[3]
0{4}
key: "pubmed://database/info"
kind: "resource"
mime_type: "application/json"
fingerprint: "e301a686e051642ff47a323ddbe64e9b3d0db907cd18ca97eb7647ac2a3f4762"
1{4}
key: "skill://pubmed-guide/SKILL.md"
kind: "resource"
mime_type: "text/markdown"
fingerprint: "4ce1762272afafbc83c331ca9da4876bae25e426a993b0115dd0433347f7c701"
2{4}
key: "skill://{+path}"
kind: "template"
mime_type: null
fingerprint: "9777dc7f1cf468158c157032a0ccebf9b50270f4e8753af9ccaf2fe99890ccf0"
prompts[1]
0{2}
name: "research_plan"
fingerprint: "7c7426437a8d9ee95ca13a909bda9286140bfe31aa3da5e7aed710d278606a21"
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: "pubmed.caseyjhand.com"
registrable_domain: "caseyjhand.com"
source: "transport"
findings[16]
0{6}
check_id: "SQ-SERVER-AUTH-NONE-WRITE"
category: "authentication"
severity: "MEDIUM"
title: "State-changing tools available without authentication"
subject_type: "server"
subject_name: null
1{6}
check_id: "SQ-TOOL-ANNOTATION-UNDERCLAIM"
category: "annotations"
severity: "MEDIUM"
title: "Annotations understate what the tool does"
subject_type: "tool"
subject_name: "pubmed_search_articles"
2{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "pubmed_europepmc_search"
3{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "pubmed_fetch_articles"
4{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "pubmed_fetch_fulltext"
5{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "pubmed_format_citations"
6{6}
check_id: "SQ-TOOL-CROSS-TOOL-REFERENCE"
category: "prompt_injection"
severity: "MEDIUM"
title: "Gives instructions about other tools"
subject_type: "tool"
subject_name: "pubmed_europepmc_search"
7{6}
check_id: "SQ-TOOL-CROSS-TOOL-REFERENCE"
category: "prompt_injection"
severity: "MEDIUM"
title: "Gives instructions about other tools"
subject_type: "tool"
subject_name: "pubmed_lookup_mesh"
8{6}
check_id: "SQ-TOOL-CROSS-TOOL-REFERENCE"
category: "prompt_injection"
severity: "MEDIUM"
title: "Gives instructions about other tools"
subject_type: "tool"
subject_name: "pubmed_search_articles"
9{6}
check_id: "SQ-TOOL-CROSS-TOOL-REFERENCE"
category: "prompt_injection"
severity: "MEDIUM"
title: "Gives instructions about other tools"
subject_type: "tool"
subject_name: "pubmed_spell_check"
10{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: "pubmed_europepmc_search"
11{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: "pubmed_lookup_mesh"
12{6}
check_id: "SQ-TOOL-LENGTH-ANOMALY"
category: "tool_design"
severity: "LOW"
title: "Unusually long model-facing text"
subject_type: "tool"
subject_name: "pubmed_fetch_fulltext"
13{6}
check_id: "SQ-TOOL-MIXED-SCRIPT"
category: "deceptive_metadata"
severity: "MEDIUM"
title: "Look-alike characters from mixed scripts"
subject_type: "tool"
subject_name: "pubmed_fetch_articles"
14{6}
check_id: "SQ-TOOL-OVERLY-BROAD"
category: "tool_design"
severity: "MEDIUM"
title: "Runs arbitrary code with open-world access"
subject_type: "tool"
subject_name: "pubmed_search_articles"
15{6}
check_id: "SQ-TOOL-TITLE-EFFECT-MISMATCH"
category: "deceptive_metadata"
severity: "HIGH"
title: "Display title describes a lower-impact action than the name"
subject_type: "tool"
subject_name: "pubmed_search_articles"
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/pubmed-mcp-server"
registry_content_sha256: "f32e42a4f4e8fe3828435cd5fb6e1b51e5ccf2f1925202252c6b40772cdfaf05"
scan_snapshot_fingerprint: "6141c42c897cdb1ac9f3bab7e0c2d057472464969b3e77c42db45afdce0faf79"
scanner_version: "1.0.0"
timestamps{4}
generated_at: "2026-11-15T02:14:20.668Z"
observed_at: "2026-11-13T18:40:41.147+00:00"
registry_published_at: "2026-11-13T15:01:30.537167+00:00"
registry_updated_at: null