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Biolab MCP Server

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io.github.srikarjy/biolab-mcp-serverv0.3.0

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

Health & Science Research & Knowledge

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add_evidence_to_collection

Add or update a retrieval in a scientist-reviewed evidence collection.

retrieval_idstring, required

collection_idstring, required

notestring

relevancestring

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Tools (30)

add_evidence_to_collection

Add or update a retrieval in a scientist-reviewed evidence collection.

Argument	Type	Description
note	string
relevance	string
retrieval_id*	string
collection_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "add_evidence_to_collectionArguments",
  "required": [
    "collection_id",
    "retrieval_id"
  ],
  "properties": {
    "note": {
      "type": "string",
      "title": "Note",
      "default": ""
    },
    "relevance": {
      "type": "string",
      "title": "Relevance",
      "default": "unreviewed"
    },
    "retrieval_id": {
      "type": "string",
      "title": "Retrieval Id"
    },
    "collection_id": {
      "type": "string",
      "title": "Collection Id"
    }
  }
}

create_claim

Create a scientific claim record without asserting that it is true.

Argument	Type	Description
claim*	string
project_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "create_claimArguments",
  "required": [
    "project_id",
    "claim"
  ],
  "properties": {
    "claim": {
      "type": "string",
      "title": "Claim"
    },
    "project_id": {
      "type": "string",
      "title": "Project Id"
    }
  }
}

create_evidence_collection

Create a reviewed evidence collection in a project.

Argument	Type	Description
name*	string
project_id*	string
description	string

Input schema (JSON)

{
  "type": "object",
  "title": "create_evidence_collectionArguments",
  "required": [
    "project_id",
    "name"
  ],
  "properties": {
    "name": {
      "type": "string",
      "title": "Name"
    },
    "project_id": {
      "type": "string",
      "title": "Project Id"
    },
    "description": {
      "type": "string",
      "title": "Description",
      "default": ""
    }
  }
}

create_evidence_watch

Create a saved query for explicit evidence-change monitoring.

Argument	Type	Description
query*	string
source*	string
agent_id*	string
project_id*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "create_evidence_watchArguments",
  "required": [
    "project_id",
    "source",
    "query",
    "agent_id"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    },
    "source": {
      "type": "string",
      "title": "Source"
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "project_id": {
      "type": "string",
      "title": "Project Id"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "default": 10
    }
  }
}

create_project

Create a persistent scientist research project.

Argument	Type	Description
name*	string
description	string

Input schema (JSON)

{
  "type": "object",
  "title": "create_projectArguments",
  "required": [
    "name"
  ],
  "properties": {
    "name": {
      "type": "string",
      "title": "Name"
    },
    "description": {
      "type": "string",
      "title": "Description",
      "default": ""
    }
  }
}

fetch

Fetch one preserved evidence record by retrieval ID.

read-only

Argument	Type	Description
id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "plugin_fetchArguments",
  "required": [
    "id"
  ],
  "properties": {
    "id": {
      "type": "string",
      "title": "Id"
    }
  }
}

get_artifact

Fetch an output artifact by its sha256 (text only; capped in size).

read-only

Argument	Type	Description
sha256*	string

Input schema (JSON)

{
  "type": "object",
  "title": "get_artifactArguments",
  "required": [
    "sha256"
  ],
  "properties": {
    "sha256": {
      "type": "string",
      "title": "Sha256"
    }
  }
}

get_evidence_collection

Return a collection and its reviewed evidence items.

read-only

Argument	Type	Description
collection_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "get_evidence_collectionArguments",
  "required": [
    "collection_id"
  ],
  "properties": {
    "collection_id": {
      "type": "string",
      "title": "Collection Id"
    }
  }
}

get_execution

Fetch one execution record, including output artifact hashes.

read-only

Argument	Type	Description
execution_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "get_executionArguments",
  "required": [
    "execution_id"
  ],
  "properties": {
    "execution_id": {
      "type": "string",
      "title": "Execution Id"
    }
  }
}

get_project_report

Return collections, claims, evidence links, watches, and events for a project.

read-only

Argument	Type	Description
project_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "get_project_reportArguments",
  "required": [
    "project_id"
  ],
  "properties": {
    "project_id": {
      "type": "string",
      "title": "Project Id"
    }
  }
}

get_retrieval

Retrieve a full retrieval record by its retrieval_id. Args: retrieval_id: the UUID returned by search_pubmed

read-only

Argument	Type	Description
retrieval_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "get_retrievalArguments",
  "required": [
    "retrieval_id"
  ],
  "properties": {
    "retrieval_id": {
      "type": "string",
      "title": "Retrieval Id"
    }
  }
}

link_claim_evidence

Propose or record how one retrieval relates to a claim.

Argument	Type	Description
note	string
stance*	string
claim_id*	string
assessment	string
retrieval_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "link_claim_evidenceArguments",
  "required": [
    "claim_id",
    "retrieval_id",
    "stance"
  ],
  "properties": {
    "note": {
      "type": "string",
      "title": "Note",
      "default": ""
    },
    "stance": {
      "type": "string",
      "title": "Stance"
    },
    "claim_id": {
      "type": "string",
      "title": "Claim Id"
    },
    "assessment": {
      "type": "string",
      "title": "Assessment",
      "default": "agent_proposed"
    },
    "retrieval_id": {
      "type": "string",
      "title": "Retrieval Id"
    }
  }
}

list_evidence_collections

List evidence collections, optionally within one project.

read-only

Argument	Type	Description
project_id	any

Input schema (JSON)

{
  "type": "object",
  "title": "list_evidence_collectionsArguments",
  "properties": {
    "project_id": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "title": "Project Id",
      "default": null
    }
  }
}

list_evidence_events

List change events previously detected by an evidence watch.

read-only

Argument	Type	Description
watch_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "list_evidence_eventsArguments",
  "required": [
    "watch_id"
  ],
  "properties": {
    "watch_id": {
      "type": "string",
      "title": "Watch Id"
    }
  }
}

list_evidence_watches

List saved evidence watches, optionally within one project.

read-only

Argument	Type	Description
project_id	any

Input schema (JSON)

{
  "type": "object",
  "title": "list_evidence_watchesArguments",
  "properties": {
    "project_id": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "title": "Project Id",
      "default": null
    }
  }
}

list_execution_tools

List runnable tools with their pinned versions, containers and devices.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "title": "list_execution_toolsArguments",
  "properties": {}
}

list_executions

List recent execution records, newest first.

read-only

Argument	Type	Description
tool	any
limit	integer

Input schema (JSON)

{
  "type": "object",
  "title": "list_executionsArguments",
  "properties": {
    "tool": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "title": "Tool",
      "default": null
    },
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 50
    }
  }
}

list_projects

List scientist research projects.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "title": "list_projectsArguments",
  "properties": {}
}

replay_execution

Re-run a recorded execution and report whether its outputs reproduced. Writes nothing.

read-only

Argument	Type	Description
execution_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "replay_executionArguments",
  "required": [
    "execution_id"
  ],
  "properties": {
    "execution_id": {
      "type": "string",
      "title": "Execution Id"
    }
  }
}

run_all_evidence_watches

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

No arguments.

Input schema (JSON)

{
  "type": "object",
  "title": "run_all_evidence_watchesArguments",
  "properties": {}
}

run_evidence_watch

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

Argument	Type	Description
watch_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "run_evidence_watchArguments",
  "required": [
    "watch_id"
  ],
  "properties": {
    "watch_id": {
      "type": "string",
      "title": "Watch Id"
    }
  }
}

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 was derived from, for provenance links

Argument	Type	Description
tool*	string
inputs*	object
agent_id*	string
retrieval_ids	any

Input schema (JSON)

{
  "type": "object",
  "title": "run_toolArguments",
  "required": [
    "tool",
    "inputs",
    "agent_id"
  ],
  "properties": {
    "tool": {
      "type": "string",
      "title": "Tool"
    },
    "inputs": {
      "type": "object",
      "title": "Inputs",
      "additionalProperties": true
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "retrieval_ids": {
      "anyOf": [
        {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        {
          "type": "null"
        }
      ],
      "title": "Retrieval Ids",
      "default": null
    }
  }
}

Search all evidence sources for ChatGPT/Codex knowledge compatibility.

Argument	Type	Description
query*	string

Input schema (JSON)

{
  "type": "object",
  "title": "plugin_searchArguments",
  "required": [
    "query"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    }
  }
}

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: how many preprints to retrieve (default 5) server: "biorxiv" or "medrxiv" (default "biorxiv")

Argument	Type	Description
server	string
agent_id*	string
category*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "search_biorxivArguments",
  "required": [
    "category",
    "agent_id"
  ],
  "properties": {
    "server": {
      "type": "string",
      "title": "Server",
      "default": "biorxiv"
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "category": {
      "type": "string",
      "title": "Category"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "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)

Argument	Type	Description
query*	string
agent_id*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "search_clinicaltrialsArguments",
  "required": [
    "query",
    "agent_id"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "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)

Argument	Type	Description
query*	string
agent_id*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "search_europepmcArguments",
  "required": [
    "query",
    "agent_id"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "default": 5
    }
  }
}

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 source (1-50)

Argument	Type	Description
query*	string
sources	any
agent_id*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "search_evidenceArguments",
  "required": [
    "query",
    "agent_id"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    },
    "sources": {
      "anyOf": [
        {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        {
          "type": "null"
        }
      ],
      "title": "Sources",
      "default": null
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "default": 5
    }
  }
}

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)

Argument	Type	Description
query*	string
agent_id*	string
max_results	integer

Input schema (JSON)

{
  "type": "object",
  "title": "search_pubmedArguments",
  "required": [
    "query",
    "agent_id"
  ],
  "properties": {
    "query": {
      "type": "string",
      "title": "Query"
    },
    "agent_id": {
      "type": "string",
      "title": "Agent Id"
    },
    "max_results": {
      "type": "integer",
      "title": "Max Results",
      "default": 5
    }
  }
}

trace_claim

Trace a claim to supporting, conflicting, contextual, or insufficient evidence.

read-only

Argument	Type	Description
claim_id*	string

Input schema (JSON)

{
  "type": "object",
  "title": "trace_claimArguments",
  "required": [
    "claim_id"
  ],
  "properties": {
    "claim_id": {
      "type": "string",
      "title": "Claim Id"
    }
  }
}

verify_executions

Verify the execution hash chain and that every output artifact is intact.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "title": "verify_executionsArguments",
  "properties": {}
}