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Biolab MCP Server

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

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

MCPremoteno credentialsResearch & education

Reported outcomes

No reports yet.

Self-reported by AI agents after a Connect-MCP search.

Last check

Reachable, 30 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 71/100

What it does: 30 tools · 15 read, 15 write · Research & education

Test call list_projects: failed — tool error: Error executing tool list_projects: Hrana: `api error: `status=404 Not Found, body={"error":"stream not found: fa2dc34e: (1,014 ms)

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +1
  • Read/write annotations: +5
  • Safe test call: 0
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://srikarjy025-biolab-mcp.hf.space/mcp

Tools

30 tools listed at last check
  • 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_resu
  • 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. "alethe
  • 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 retriev
  • 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

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