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Biolab MCP Server

by srikarjy · remote · no sign-in to list tools · v0.3.0 · published by GitHub user srikarjy

Auditable MCP server for PubMed, Europe PMC, ClinicalTrials.gov, and bioRxiv/medRxiv queries

Changes · 18
CompareRegistry entry

30 tools: 18 change things and 12 only read.

Scanned Oct 21, 2026

6 checks matched something in the tool definitions. No finding is not a safety guarantee. How the checks work.

claude mcp add --transport http biolab https://srikarjy025-biolab-mcp.hf.space/mcp

Findings

Matches of fixed checks, with the text they matched.

6 warn
  • Warnsearch_evidence

    The server marks "search_evidence" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_evidence" says "search": a word for reading.

    What this check looks for
  • Warnsearch

    The server marks "search" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search" says "search": a word for reading.

    What this check looks for
  • Warnsearch_pubmed

    The server marks "search_pubmed" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_pubmed" says "search": a word for reading.

    What this check looks for
  • Warnsearch_europepmc

    The server marks "search_europepmc" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_europepmc" says "search": a word for reading.

    What this check looks for
  • Warnsearch_clinicaltrials

    The server marks "search_clinicaltrials" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_clinicaltrials" says "search": a word for reading.

    What this check looks for
  • Warnsearch_biorxiv

    The server marks "search_biorxiv" as not read-only (readOnlyHint: false), and its words say it reads.

    Matched text

    annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_biorxiv" says "search": a word for reading.

    What this check looks for

Tools

Open a tool for its reasons and full description. Descriptions are the publisher's own words, shown as they are.

30 tools

Changes things 18Claude Code: ask
  • add_evidence_to_collectionAdd or update a retrieval in a scientist-reviewed evidence collection.No findings

    Why it is in this group

    • The name "add_evidence_to_collection" says "add": a word for a change.
    Description, as the server wrote it
    Add or update a retrieval in a scientist-reviewed evidence collection.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • create_claimCreate a scientific claim record without asserting that it is true.No findings

    Why it is in this group

    • The name "create_claim" says "create": a word for a change.
    Description, as the server wrote it
    Create a scientific claim record without asserting that it is true.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • create_evidence_collectionCreate a reviewed evidence collection in a project.No findings

    Why it is in this group

    • The name "create_evidence_collection" says "create": a word for a change.
    Description, as the server wrote it
    Create a reviewed evidence collection in a project.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • create_evidence_watchCreate a saved query for explicit evidence-change monitoring.No findings

    Why it is in this group

    • The name "create_evidence_watch" says "create": a word for a change.
    Description, as the server wrote it
    Create a saved query for explicit evidence-change monitoring.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • create_projectCreate a persistent scientist research project.No findings

    Why it is in this group

    • The name "create_project" says "create": a word for a change.
    Description, as the server wrote it
    Create a persistent scientist research project.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • replay_executionRe-run a recorded execution and report whether its outputs reproduced.No 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.
    Description, as the server wrote it
    Re-run a recorded execution and report whether its outputs reproduced. Writes nothing.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • run_all_evidence_watchesRun all active watches and return explicit per-watch failures.Reads text others writeNo findings

    Why it is in this group

    • The name "run_all_evidence_watches" says "run": a word for a change.

    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
    Run all active watches and return explicit per-watch failures.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • run_evidence_watchRun one evidence watch and record added, removed, or revised evidence.Reads text others writeNo findings

    Why it is in this group

    • The name "run_evidence_watch" says "run": a word for a change.

    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
    Run one evidence watch and record added, removed, or revised evidence.

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • run_toolRun a registered tool and seal an ExecutionRecord (inputs, versions, output hashes).No findings

    Why it is in this group

    • The name "run_tool" says "run": a word for a change.
    Description, as the server wrote it
    Run a registered tool and seal an ExecutionRecord (inputs, versions, output hashes). Args: tool: tool name from list_execution_tools inputs: tool inputs (JSON object); stored verbatim so the run can be replayed agent_id: calling agent or workflow identity retrieval_ids: evidence retrievals this run was derived from, for provenance links

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: false
  • search_biorxivList bioRxiv/medRxiv preprints by category and log each to the audit trail.Reads text others write1 finding

    Why it is in this group

    • The name "search_biorxiv" says "search": a word for reading.
    • The server marks it as not read-only (readOnlyHint: false).

    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 "search_biorxiv" as not read-only (readOnlyHint: false), and its words say it reads.

      Matched text

      annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_biorxiv" says "search": a word for reading.

      What this check looks for
    Description, as the server wrote it
    List bioRxiv/medRxiv preprints by category and log each to the audit trail. No free-text search exists on this API — only category listing (last 30 days). Args: category: category, e.g. "neuroscience", "bioinformatics", or "all" agent_id: which agent is asking, e.g. "aletheia:advocate" max_results: how many preprints to retrieve (default 5) server: "biorxiv" or "medrxiv" (default "biorxiv")

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • search_clinicaltrialsSearch ClinicalTrials.gov and log every retrieved study to the audit trail.Reads text others write1 finding

    Why it is in this group

    • The name "search_clinicaltrials" says "search": a word for reading.
    • The server marks it as not read-only (readOnlyHint: false).

    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 "search_clinicaltrials" as not read-only (readOnlyHint: false), and its words say it reads.

      Matched text

      annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_clinicaltrials" says "search": a word for reading.

      What this check looks for
    Description, as the server wrote it
    Search ClinicalTrials.gov and log every retrieved study to the audit trail. Args: query: condition/disease search string, sent to ClinicalTrials.gov verbatim agent_id: which agent is asking, e.g. "aletheia:advocate" max_results: how many studies to retrieve (default 5)

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • search_europepmcSearch Europe PMC and log every retrieved article to the audit trail.Reads text others write1 finding

    Why it is in this group

    • The name "search_europepmc" says "search": a word for reading.
    • The server marks it as not read-only (readOnlyHint: false).

    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 "search_europepmc" as not read-only (readOnlyHint: false), and its words say it reads.

      Matched text

      annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_europepmc" says "search": a word for reading.

      What this check looks for
    Description, as the server wrote it
    Search Europe PMC and log every retrieved article to the audit trail. Args: query: exact search string, sent to Europe PMC verbatim — no normalization agent_id: which agent is asking, e.g. "aletheia:advocate" max_results: how many articles to retrieve (default 5)

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • search_evidenceSearch several scientific sources in one explicitly audited workflow.Reads text others write1 finding

    Why it is in this group

    • The name "search_evidence" says "search": a word for reading.
    • The server marks it as not read-only (readOnlyHint: false).

    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 "search_evidence" as not read-only (readOnlyHint: false), and its words say it reads.

      Matched text

      annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_evidence" says "search": a word for reading.

      What this check looks for
    Description, as the server wrote it
    Search several scientific sources in one explicitly audited workflow. Args: query: scientific evidence query sent to each selected source agent_id: calling agent or workflow identity sources: any of pubmed, europepmc, clinicaltrials, uniprot, opentargets max_results: maximum results to preserve per source (1-50)

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • search_pubmedSearch PubMed and log every retrieved paper to the audit trail.Reads text others write1 finding

    Why it is in this group

    • The name "search_pubmed" says "search": a word for reading.
    • The server marks it as not read-only (readOnlyHint: false).

    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 "search_pubmed" as not read-only (readOnlyHint: false), and its words say it reads.

      Matched text

      annotations: {"readOnlyHint":false,"destructiveHint":false,"idempotentHint":false,"openWorldHint":true}; The name "search_pubmed" says "search": a word for reading.

      What this check looks for
    Description, as the server wrote it
    Search PubMed and log every retrieved paper to the audit trail. Args: query: exact search string, sent to PubMed verbatim — no normalization agent_id: which agent is asking, e.g. "aletheia:advocate" max_results: how many papers to retrieve (default 5)

    Annotations the server declares

    • readOnlyHint: false
    • destructiveHint: false
    • idempotentHint: false
    • openWorldHint: true
  • trace_claimTrace a claim to supporting, conflicting, contextual, or insufficient evidence.No 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.
    Description, as the server wrote it
    Trace a claim to supporting, conflicting, contextual, or insufficient evidence.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • verify_executionsVerify the execution hash chain and that every output artifact is intact.No 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.
    Description, as the server wrote it
    Verify the execution hash chain and that every output artifact is intact.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
Only reads 12Claude Code: allow
  • fetchFetch one preserved evidence record by retrieval ID.No findings

    Why it is in this group

    • The name "fetch" says "fetch": a word for reading.
    Description, as the server wrote it
    Fetch one preserved evidence record by retrieval ID.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • get_artifactFetch an output artifact by its sha256 (text only; capped in size).No findings

    Why it is in this group

    • The name "get_artifact" says "get": a word for reading.
    Description, as the server wrote it
    Fetch an output artifact by its sha256 (text only; capped in size).

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • get_evidence_collectionReturn a collection and its reviewed evidence items.No findings

    Why it is in this group

    • The name "get_evidence_collection" says "get": a word for reading.
    Description, as the server wrote it
    Return a collection and its reviewed evidence items.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • get_executionFetch one execution record, including output artifact hashes.No findings

    Why it is in this group

    • The name "get_execution" says "get": a word for reading.
    Description, as the server wrote it
    Fetch one execution record, including output artifact hashes.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • get_project_reportReturn collections, claims, evidence links, watches, and events for a project.No findings

    Why it is in this group

    • The name "get_project_report" says "get": a word for reading.
    Description, as the server wrote it
    Return collections, claims, evidence links, watches, and events for a project.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • get_retrievalRetrieve a full retrieval record by its retrieval_id.No findings

    Why it is in this group

    • The name "get_retrieval" says "get": a word for reading.
    Description, as the server wrote it
    Retrieve a full retrieval record by its retrieval_id. Args: retrieval_id: the UUID returned by search_pubmed

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_evidence_collectionsList evidence collections, optionally within one project.No findings

    Why it is in this group

    • The name "list_evidence_collections" says "list": a word for reading.
    Description, as the server wrote it
    List evidence collections, optionally within one project.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_evidence_eventsList change events previously detected by an evidence watch.No findings

    Why it is in this group

    • The name "list_evidence_events" says "list": a word for reading.
    Description, as the server wrote it
    List change events previously detected by an evidence watch.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_evidence_watchesList saved evidence watches, optionally within one project.No findings

    Why it is in this group

    • The name "list_evidence_watches" says "list": a word for reading.
    Description, as the server wrote it
    List saved evidence watches, optionally within one project.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_execution_toolsList runnable tools with their pinned versions, containers and devices.No findings

    Why it is in this group

    • The name "list_execution_tools" says "list": a word for reading.
    Description, as the server wrote it
    List runnable tools with their pinned versions, containers and devices.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_executionsList recent execution records, newest first.No findings

    Why it is in this group

    • The name "list_executions" says "list": a word for reading.
    Description, as the server wrote it
    List recent execution records, newest first.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false
  • list_projectsList scientist research projects.No findings

    Why it is in this group

    • The name "list_projects" says "list": a word for reading.
    Description, as the server wrote it
    List scientist research projects.

    Annotations the server declares

    • readOnlyHint: true
    • destructiveHint: false
    • idempotentHint: true
    • openWorldHint: false

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 outbound.

Reads private data1
Reads files, mail, messages, databases, secrets, calendars or repositories.
Reads text others write8
Brings in text someone else can write: web pages, inbound email, messages, issues and comments.
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.

Install

Pinned to version 0.3.0. Values in angle brackets are yours to fill in.

claude mcp add --transport http biolab https://srikarjy025-biolab-mcp.hf.space/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__biolab__fetch",
      "mcp__biolab__list_projects",
      "mcp__biolab__list_evidence_collections",
      "mcp__biolab__get_evidence_collection",
      "mcp__biolab__list_evidence_watches",
      "mcp__biolab__list_evidence_events",
      "mcp__biolab__get_project_report",
      "mcp__biolab__list_execution_tools",
      "mcp__biolab__get_execution",
      "mcp__biolab__list_executions",
      "mcp__biolab__get_artifact",
      "mcp__biolab__get_retrieval"
    ],
    "ask": [
      "mcp__biolab__search_evidence",
      "mcp__biolab__search",
      "mcp__biolab__create_project",
      "mcp__biolab__create_evidence_collection",
      "mcp__biolab__add_evidence_to_collection",
      "mcp__biolab__create_evidence_watch",
      "mcp__biolab__run_evidence_watch",
      "mcp__biolab__run_all_evidence_watches",
      "mcp__biolab__create_claim",
      "mcp__biolab__link_claim_evidence",
      "mcp__biolab__trace_claim",
      "mcp__biolab__search_pubmed",
      "mcp__biolab__search_europepmc",
      "mcp__biolab__search_clinicaltrials",
      "mcp__biolab__search_biorxiv",
      "mcp__biolab__run_tool",
      "mcp__biolab__verify_executions",
      "mcp__biolab__replay_execution"
    ],
    "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 biolab. Review it before you use it.

Capability tags behind 8 rules
  • mcp__biolab__search_evidence untrusted-input
  • mcp__biolab__search private-data, untrusted-input
  • mcp__biolab__run_evidence_watch untrusted-input
  • mcp__biolab__run_all_evidence_watches untrusted-input
  • mcp__biolab__search_pubmed untrusted-input
  • mcp__biolab__search_europepmc untrusted-input
  • mcp__biolab__search_clinicaltrials untrusted-input
  • mcp__biolab__search_biorxiv untrusted-input