Pathways containing an entity, looked up by external resource id (e.g. UniProt accession).
Part of the Reactome server.
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AI agents call pathways_for_entity to retrieve information from Reactome without modifying any data. This is common in research, monitoring, and reporting workflows where the agent needs context before taking action. Because read operations don't change state, they are generally safe to allow without restrictions -- but you may still want rate limits to control API costs.
Even though pathways_for_entity only reads data, uncontrolled read access can leak sensitive information or rack up API costs. An agent caught in a retry loop could make thousands of calls per minute. A rate limit gives you a safety net without blocking legitimate use.
Read-only tools are safe to allow by default. No rate limit needed unless you want to control costs.
{
"version": "1",
"default": "deny",
"tools": {
"pathways_for_entity": {}
}
}See the full Reactome policy for all 25 tools.
These attack patterns abuse exactly the kind of access pathways_for_entity gives an agent. Each links to the full case and the policy that stops it:
Other read tools across the catalogue. The same approach applies to each: allow, with a rate cap to control cost.
Pathways containing an entity, looked up by external resource id (e.g. UniProt accession).. It is categorised as a Read tool in the Reactome MCP Server, which means it retrieves data without modifying state.
Register the Reactome MCP server in PolicyLayer and add a rule for pathways_for_entity: 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 Reactome. Nothing to install.
pathways_for_entity 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 pathways_for_entity 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 pathways_for_entity. 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.
pathways_for_entity is provided by the Reactome MCP server (https://gateway.pipeworx.io/reactome/mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Deterministic rules across all 25 Reactome tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.
Free to start. No card required.
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