biomedmcp

io.github.unibio-intelligence/biomedmcpunibio-intelligencestreamable-httpv0.2.4Scanned 1 hour ago

Integrated public biomedical research with cited, bounded evidence.

13 tools: 4 change things and 9 only read.

Reads private data · 0
Reads text others write · 11
Can send data out · 0
2 findings

Anlyon alternative

4 of these tools change something. Run those as governed actions.

Declare what an action changes, and Anlyon puts it under a shared limit, binds every approval to the exact request, and grades the outcome. It works on any HTTPS API you can describe as an action.

Anlyon does not run, proxy or govern this MCP server. A tool your own code calls directly is not routed through Anlyon and is not governed by it.

Import an OpenAPI spec →

Tools

Grouped by what each tool does, most consequential first. Open one for its reasons and full description; descriptions are the publisher's own words.

13 tools

Changes things 4Creates or changes something that can be changed back.Claude Code: ask

batchExecute up to ten independent read operations with one atomic quota reservation.Reads text others write1 finding
Why it is in this group
- The description's first verb is "execute": a word for a change.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Findings
- Warn
  The server marks "batch" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
  Matched text
  annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The description's first verb is "execute": a word for a change.
  What this check looks for
Description, as the server wrote it
Execute up to ten independent read operations with one atomic quota reservation. e.g. {"calls":[{"operation":"get","arguments":{"entity":"gene","id":"BRAF","species":9606}}]}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
query_sourceRun advanced source operations after checking capabilities/schema.Reads text others write1 finding
Why it is in this group
- The name "query_source" says "query": a word for reading.
- The description's first verb is "run": a word for a change.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Findings
- Warn
  The server marks "query_source" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
  Matched text
  annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The name "query_source" says "query": a word for reading.
  What this check looks for
Description, as the server wrote it
Run advanced source operations after checking capabilities/schema. Common tasks have dedicated tools. e.g. {"source":"gtex","operation":"get_metadata","params":{"info_type":"tissues","dataset_id":"gtex_v10"}}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
relateTraverse an evidence relationship.Reads text others writeNo findings
Why it is in this group
- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Traverse an evidence relationship. Relations: gene/drug/disease: articles,trials; variant: articles,structure; article: citations,references,recommendations,authors,entities; author: articles. e.g. {"entity":"article","id":"PMID:123","relation":"references"}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
researchDossiers retain citations/outcomes.Reads text others writeNo findings
Why it is in this group
- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Dossiers retain citations/outcomes. Inspect capabilities and get further sections for completeness. e.g. {"workflow":"target_dossier","focus":"ERBB2","species":9606}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true

Only reads 9Looks things up and changes nothing.Show 9 read-only tools

capabilitiesInspect enabled sources, workflows, sections or an advanced operation's exact schema.No findings
Why it is in this group
- The description's first verb is "inspect": a word for reading.
Description, as the server wrote it
Inspect enabled sources, workflows, sections or an advanced operation's exact schema. e.g. {}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
getRead ordinary records/evidence sections; variants use variant_evidence.Reads text others writeNo findings
Why it is in this group
- The name "get" says "get": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Read ordinary records/evidence sections; variants use variant_evidence. Sources constrain all lookups and identity dependencies. e.g. {"entity":"gene","id":"BRAF","species":9606}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
literature_searchFind papers with publication/topic/source filters; deduplicate evidence and retain source outcomes and opaque continuation.Reads text others writeNo findings
Why it is in this group
- The name "literature_search" says "search": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Find papers with publication/topic/source filters; deduplicate evidence and retain source outcomes and opaque continuation. e.g. {"query":"KRAS resistance"}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
quotaInspect current research allowance and reset times; sign in for higher limits.No findings
Why it is in this group
- The description's first verb is "inspect": a word for reading.
Description, as the server wrote it
Inspect current research allowance and reset times; sign in for higher limits. e.g. {}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
resolveResolve aliases/ambiguity before evidence joins.Reads text others writeNo findings
Why it is in this group
- The name "resolve" says "resolve": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Resolve aliases/ambiguity before evidence joins. One exact species-qualified symbol/ID resolves; provider score alone never establishes identity. Retrieve known unambiguous identifiers directly. e.g. {"entity":"gene","query":"HER2","species":9606}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
searchFind ordinary records with entity filters.Reads text others writeNo findings
Why it is in this group
- The name "search" says "search": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Find ordinary records with entity filters. Papers use literature_search; trials use trial_search. e.g. {"entity":"gene","query":"BRCA1","filters":{"species":9606}}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
study_analysisAnalyze an installed verified public study.Reads text others writeNo findings
Why it is in this group
- The description's first verb is "analyze": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Analyze an installed verified public study. Bundled ubi_synthetic is an invented demo; discover installed releases with capabilities(source=study). Report clinical and assayed samples separately, unique mutant samples, events and exclusions. Preserve input hashes and denominators. Private compute uses Ubi platform. e.g. {"analysis":"gene_profile","study":"ubi_synthetic","gene":"TP53"}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
trial_searchFind public clinical trials using disease/intervention and trial-specific filters.Reads text others writeNo findings
Why it is in this group
- The name "trial_search" says "search": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Find public clinical trials using disease/intervention and trial-specific filters. Does not determine individual clinical eligibility. e.g. {"query":"melanoma","filters":{"status":"RECRUITING"}}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
variant_evidenceRetrieve variant evidence with assembly/transcript ambiguity preserved.Reads text others writeNo findings
Why it is in this group
- The description's first verb is "retrieve": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
Retrieve variant evidence with assembly/transcript ambiguity preserved. Defaults: ClinVar, population, CIViC. Request predictions for AlphaMissense, or eve for MIT-licensed EVE protein scores; computational predictions retain source and uncertainty. e.g. {"id":"BRAF V600E"}; biomedmcp://guide
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true

This is not a safety rating, and no finding is not a safety guarantee. The groups and findings come from fixed checks of the tool definitions the server returned on the date shown, not from its code or what it does when called. How the checks work.

Exfil surface

Which tools read private data, which read text someone else can write, and which can send data out. One of each is a path a prompt injection can use.

No private-data, untrusted-input, outbound path in this server alone: no tool is tagged private-data or outbound.

Reads private data0: Reads files, mail, messages, databases, secrets, calendars or repositories.
Reads text others write11: Brings in text someone else can write: web pages, inbound email, messages, issues and comments.; batch
get
literature_search
query_source
relate
research
resolve
search
study_analysis
trial_search
variant_evidence
Can send data out0: Can carry data to people or systems: it sends, posts or publishes, or takes a recipient, channel or URL.

Other servers in the same agent add their own tools to these paths. Audit your whole setup to see them together.

Findings

Matches of fixed checks, with the text they matched.

2 warn

Warnquery_source
The server marks "query_source" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
Matched text
annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The name "query_source" says "query": a word for reading.
What this check looks for
Warnbatch
The server marks "batch" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
Matched text
annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The description's first verb is "execute": a word for a change.
What this check looks for

History

Changes to its tool definitions and to its remote endpoint, newest first.

No change seen yet. Its tools are rescanned every day, and a remote endpoint is looked at once a week.

All changes to this server

Install

Pinned to version 0.2.4. Values in angle brackets are yours to fill in.

claude mcp add --transport http biomedmcp https://biomedmcp.unibiointelligence.com/mcp

claude mcp add --transport http biomedmcp https://biomedmcp.unibiointelligence.com/mcp

Run in a terminal.

Claude Code permissions

Allow the reads, ask before a change or a way out, deny the deletes. Paste into .claude/settings.json.

.claude/settings.json

{
  "permissions": {
    "allow": [
      "mcp__biomedmcp__search",
      "mcp__biomedmcp__get",
      "mcp__biomedmcp__literature_search",
      "mcp__biomedmcp__trial_search",
      "mcp__biomedmcp__variant_evidence",
      "mcp__biomedmcp__study_analysis",
      "mcp__biomedmcp__resolve",
      "mcp__biomedmcp__capabilities",
      "mcp__biomedmcp__quota"
    ],
    "ask": [
      "mcp__biomedmcp__relate",
      "mcp__biomedmcp__research",
      "mcp__biomedmcp__query_source",
      "mcp__biomedmcp__batch"
    ],
    "deny": []
  }
}

Tools that only read are allowed, tools that change things ask first, tools that delete or cancel are denied. A read that can send data out (it takes a URL, say) asks first too. It assumes the server is installed as biomedmcp. Review it before you use it.

Capability tags behind 11 rules

mcp__biomedmcp__search untrusted-input
mcp__biomedmcp__get untrusted-input
mcp__biomedmcp__literature_search untrusted-input
mcp__biomedmcp__trial_search untrusted-input
mcp__biomedmcp__variant_evidence untrusted-input
mcp__biomedmcp__study_analysis untrusted-input
mcp__biomedmcp__resolve untrusted-input
mcp__biomedmcp__relate untrusted-input
mcp__biomedmcp__research untrusted-input
mcp__biomedmcp__query_source untrusted-input
mcp__biomedmcp__batch untrusted-input

Keep the decision: fail CI when the tools change, follow every change, or show a badge.

Pin in CI

Fail a build when the tools you reviewed are not the tools the server serves today.

curl -s "https://anlyon.dev/api/v1/servers/io.github.unibio-intelligence/biomedmcp/verify?hash=727f8416fc326138cbfbbde9fe5a820105f57b9ad9379d24a04ef951cc722211" | jq -e '.changed == false'

Pinned hash 727f8416fc32, from Nov 5, 2026, 05:18 UTC.

Watch

Get told when its tools change: a new tool, a new description, a new class.

https://anlyon.dev/servers/io.github.unibio-intelligence/biomedmcp/changes.xml

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Badge

[![anlyon.dev](https://anlyon.dev/badge/io.github.unibio-intelligence/biomedmcp.svg)](https://anlyon.dev/servers/io.github.unibio-intelligence/biomedmcp)

Source: MCP Registry · repository. Synced Nov 5, 2026, 05:18 UTC.