AI agents call get_compounds_by_formula 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 appears designed to retrieve or query compounds from a biomedical database filtered by chemical formula. This is consistent with Read category operations—it retrieves information without modifying state or executing arbitrary code. The empty description and lack of explicit mutation capability lower severity to low.
From the tool's definition Tool name 'get_compounds_by_formula' indicates retrieval of compound data based on a chemical formula query. The naming pattern matches other sibling tools that are all Read operations (check_*, get_*, query_*).
Documented attack patterns abuse exactly the kind of access get_compounds_by_formula 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_compounds_by_formula:
{
"version": "1",
"default": "deny",
"tools": {
"get_compounds_by_formula": {}
}
}get_compounds_by_formula is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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get_compounds_by_formula. 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_compounds_by_formula: 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_compounds_by_formula 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_compounds_by_formula 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_compounds_by_formula. 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_compounds_by_formula 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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439 OrigeneMCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.