Return data for a specific reference in GA4GH format by id
AI agents call get_ga4gh_references to retrieve information from OrigeneMCP without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool retrieves genomic reference data by identifier and returns it in GA4GH (Global Alliance for Genomics and Health) format. It performs a read-only query operation without side effects, making it a Read category tool. The severity is low as retrieving public genomic reference data poses minimal risk even if accessed inappropriately.
From the tool's definition Tool name 'get_ga4gh_references' and description 'Return data for a specific reference in GA4GH format by id' indicate a retrieval operation. The use of 'Return' and 'get' confirms data querying with no modification or deletion.
Documented attack patterns abuse exactly the kind of access get_ga4gh_references gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and OrigeneMCP, and nothing reaches the server without passing your rules. This is the rule we recommend for get_ga4gh_references:
{
"version": "1",
"default": "deny",
"tools": {
"get_ga4gh_references": {}
}
}get_ga4gh_references is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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Return data for a specific reference in GA4GH format by id. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.
Register the Origene MCP server in PolicyLayer and add a rule for get_ga4gh_references: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches OrigeneMCP. Nothing to install.
get_ga4gh_references is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the get_ga4gh_references rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for get_ga4gh_references. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
get_ga4gh_references is provided by the Origene MCP server (gentel-lab/origenemcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from OrigeneMCP, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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