// SCAN REPORT

AGR MCP Server

26 tools. 6 can modify or destroy data without limits.

1 destructive tool with no built-in limits. Policy required.

Last updated: 4 Jul 2026

6 can modify or destroy data

20 read-only

26 tools total

Community server · catalogue entry verified 04/07/2026

How to control AGR MCP Server ↓

TOOL MAP

What AGR MCP Server exposes to your agents

Read (20) Write / Execute (5) Destructive / Financial (1)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

Critical Risk

The most dangerous AGR MCP Server tools

Destructive · High mine_delete_list This tool permanently removes data (a list) from AllianceMine and cannot be undone. Execute · Medium mine_run_template Although this tool queries genomics data (which would normally be 'Read'), the use of 'run' and 'template' with parameters indicates execution of pre-defined operations whose behavior depends on supplied arguments. Execute · High mine_query This tool executes raw, user-supplied PathQuery XML against the AllianceMine InterMine database. Execute · High mine_query_builder Although the server is read-oriented (genomics data retrieval), this tool accepts a flexible JSON DSL and executes it against AllianceMine.

6 of AGR MCP Server's 26 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control AGR MCP Server

PolicyLayer is an MCP gateway — it sits between your AI agents and AGR MCP Server, and nothing reaches the server without passing your rules. These are the rules we recommend:

Deny destructive operations

{
  "mine_delete_list": {
    "deny_if": [
      {
        "conditions": [],
        "on_deny": "Blocked by default. Requires approval."
      }
    ]
  }
}

Destructive tools should never be available to autonomous agents without human approval.

Rate limit write operations

{
  "mine_add_to_list": {
    "limits": [
      {
        "counter": "mine_add_to_list_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "find_orthologs": {
    "limits": [
      {
        "counter": "find_orthologs_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register AGR MCP Server — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON AGR →

Instant setup, no code required.

FULL CATALOGUE

All 26 AGR MCP Server tools

DESTRUCTIVE 1 tools

Destructive mine_delete_list Delete a list from AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable.

EXECUTE 3 tools

Execute mine_query Run a raw PathQuery XML query against AllianceMine. For power users who know InterMine PathQuery syntax. Execute mine_query_builder Build and run structured queries against AllianceMine using a JSON DSL. Example query - find human genes in D Execute mine_run_template Run a pre-built query template with parameters. Parameter format: Use numeric keys (

WRITE 2 tools

Write mine_add_to_list Add items to an existing list. Requires ALLIANCEMINE_TOKEN environment variable. Write mine_create_list Create a new list in AllianceMine. Requires ALLIANCEMINE_TOKEN environment variable.

READ 20 tools

Read find_orthologs Find orthologous genes across species. Returns homologs from all Alliance model organisms. Read find_paralogs Find paralogous genes within the same species (genes related by duplication). Complements find_orthologs. Read get_allele_info Get detailed information about a specific allele/variant by its identifier. Read get_disease_info Get detailed information about a disease by its Disease Ontology ID (DOID). Read get_gene_alleles Get alleles/variants associated with a gene. Read get_gene_diseases Get disease associations for a gene, including human disease models and annotations. Read get_gene_expression Get expression data for a gene including tissue/cell type expression and developmental stages. Read get_gene_info Get detailed information about a specific gene including symbol, name, location, species, and cross-references Read get_gene_interactions Get molecular and genetic interactions for a gene. Read get_gene_models Get affected genomic models (e.g., disease models) associated with a gene. Read get_gene_phenotypes Get phenotype annotations for a gene. Read get_species_list Get list of model organisms supported by Alliance of Genome Resources. Read mine_get_list Get the contents of a specific list. Read mine_get_lists Get all available gene/protein lists in AllianceMine. Read mine_list_templates List available query templates in AllianceMine. Templates are pre-built queries for common use cases. Read mine_natural_query Process a natural language query and return schema information to construct a structured AllianceMine query. Read mine_search Search AllianceMine for genes, proteins, diseases, and other biological entities using keyword search. Read search_alleles Search for alleles/variants in the Alliance database. Read search_diseases Search for diseases in the Alliance database. Read search_genes Search for genes across all Alliance of Genome Resources model organisms. Supports species filtering.

EXPLORE

Related servers

Other MCP servers with similar tools — same risk classification, starter policies for each.

FAQ

Questions about AGR MCP Server

Can an AI agent delete data through the AGR MCP Server MCP server? +

Yes. The AGR MCP Server server exposes 1 destructive tools including mine_delete_list. These permanently remove resources with no undo. PolicyLayer blocks destructive tools by default so they never reach the upstream server.

How do I prevent bulk modifications through AGR MCP Server? +

The AGR MCP Server server has 2 write tools including mine_add_to_list, mine_create_list. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach AGR MCP Server.

How many tools does the AGR MCP Server MCP server expose? +

26 tools across 4 categories: Destructive, Execute, Read, Write. 20 are read-only. 6 can modify, create, or delete data.

How do I enforce a policy on AGR MCP Server? +

Register the AGR MCP Server MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every AGR MCP Server tool call.

Deterministic rules across all 26 AGR MCP Server tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON AGR →

Instant setup, no code required.

26 AGR MCP Server tools catalogued and risk-classified — across an index of 43,000+ MCP servers.