get_compound_structural_alert_by_id
AI agents call get_compound_structural_alert_by_id 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.
The tool appears to retrieve structural alert information for compounds identified by an ID. This is a read-only lookup operation that queries biomedical data without modification, deletion, or execution. The empty description reduces confidence slightly, but the 'get_' prefix and 'by_id' pattern strongly indicate a retrieval function rather than write, execute, or destructive operation.
From the tool's definition Tool name includes 'get_' verb indicating data retrieval; 'by_id' suggests querying a database by identifier; no description provided but naming pattern is consistent with query/lookup operations typical of biomedical databases.
Documented attack patterns abuse exactly the kind of access get_compound_structural_alert_by_id 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_compound_structural_alert_by_id:
{
"version": "1",
"default": "deny",
"tools": {
"get_compound_structural_alert_by_id": {}
}
}get_compound_structural_alert_by_id is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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get_compound_structural_alert_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_compound_structural_alert_by_id: 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_compound_structural_alert_by_id 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_compound_structural_alert_by_id 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_compound_structural_alert_by_id. 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_compound_structural_alert_by_id 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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