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Biolab MCP Server

io.github.srikarjy/biolab-mcp-server · v0.3.0

Measured by MCP Station

Description written by the publisher, not verified

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

Connect

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

{
  "mcpServers": {
    "biolab-mcp-server": {
      "url": "https://srikarjy025-biolab-mcp.hf.space/mcp"
    }
  }
}

Tools as reported by the server

• search_evidence
  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
• search
  Search all evidence sources for ChatGPT/Codex knowledge compatibility.
• fetch
  Fetch one preserved evidence record by retrieval ID.
• create_project
  Create a persistent scientist research project.
• list_projects
  List scientist research projects.
• create_evidence_collection
  Create a reviewed evidence collection in a project.
• list_evidence_collections
  List evidence collections, optionally within one project.
• add_evidence_to_collection
  Add or update a retrieval in a scientist-reviewed evidence collection.
• get_evidence_collection
  Return a collection and its reviewed evidence items.
• create_evidence_watch
  Create a saved query for explicit evidence-change monitoring.
• list_evidence_watches
  List saved evidence watches, optionally within one project.
• run_evidence_watch
  Run one evidence watch and record added, removed, or revised evidence.
• list_evidence_events
  List change events previously detected by an evidence watch.
• run_all_evidence_watches
  Run all active watches and return explicit per-watch failures.
• create_claim
  Create a scientific claim record without asserting that it is true.
• link_claim_evidence
  Propose or record how one retrieval relates to a claim.
• trace_claim
  Trace a claim to supporting, conflicting, contextual, or insufficient evidence.
• get_project_report
  Return collections, claims, evidence links, watches, and events for a project.
• search_pubmed
  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)
• search_europepmc
  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)
• search_clinicaltrials
  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)
• search_biorxiv
  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:
• list_execution_tools
  List runnable tools with their pinned versions, containers and devices.
• run_tool
  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
• get_execution
  Fetch one execution record, including output artifact hashes.
• list_executions
  List recent execution records, newest first.
• get_artifact
  Fetch an output artifact by its sha256 (text only; capped in size).
• verify_executions
  Verify the execution hash chain and that every output artifact is intact.
• replay_execution
  Re-run a recorded execution and report whether its outputs reproduced. Writes nothing.
• get_retrieval
  Retrieve a full retrieval record by its retrieval_id. Args: retrieval_id: the UUID returned by search_pubmed

Repository · Website · JSON · Text for agents · Registry updated 2026-08-15