AI agents call pdb_get_pubmed_annotations 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 (does not create, modify, delete, or execute) publicly available PubMed annotations associated with PDB (Protein Data Bank) entries. The empty description lowers confidence slightly, but the naming convention and sibling tools (all read-oriented: check, get, query, find) strongly indicate a Read operation. No side effects, no code execution, no data modification.
From the tool's definition Tool name 'pdb_get_pubmed_annotations' indicates retrieval of annotations from PubMed, a public biomedical literature database. The 'get' prefix and context within a biomedical research platform suggest data query/retrieval with no modification.
Documented attack patterns abuse exactly the kind of access pdb_get_pubmed_annotations 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 pdb_get_pubmed_annotations:
{
"version": "1",
"default": "deny",
"tools": {
"pdb_get_pubmed_annotations": {}
}
}pdb_get_pubmed_annotations is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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pdb_get_pubmed_annotations. 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 pdb_get_pubmed_annotations: 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.
pdb_get_pubmed_annotations 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 pdb_get_pubmed_annotations 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 pdb_get_pubmed_annotations. 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.
pdb_get_pubmed_annotations 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.