pdb_get_pubmed_annotations

A read tool on the Origene MCP server.

SERVEROrigeneMCP SOURCEgentel-lab/origenemcp

Low RISK CLASS

Category Read

Parameters 00 required

Recommended Allowedsee the rule below

Registry record Grade C, identity unverified Pull the record →

This record as markdown: /tools/gentel-lab-origenemcp/pdb-get-pubmed-annotations.md

WHAT IT DOES

What pdb_get_pubmed_annotations does on OrigeneMCP

AI agents call pdb_get_pubmed_annotations to retrieve information from OrigeneMCP without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

RISK

Why pdb_get_pubmed_annotations is rated Low

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.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs pdb_get_pubmed_annotations safely

PolicyLayer is an MCP gateway: it sits between your AI agents and OrigeneMCP, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For pdb_get_pubmed_annotations, this is the rule to start with:

pdb_get_pubmed_annotations Allowed

pdb_get_pubmed_annotations is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "pdb_get_pubmed_annotations": {}
  }
}

ALLOW ONLY THIS TOOL → Instant setup, no code required.

The button opens the PolicyLayer dashboard: create your workspace, connect OrigeneMCP, apply this rule, and every pdb_get_pubmed_annotations call is checked against it from then on.

FAQ

Questions about pdb_get_pubmed_annotations

What does the pdb_get_pubmed_annotations tool do? +

pdb_get_pubmed_annotations is a read tool on the Origene MCP server. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.

How do I enforce a policy on pdb_get_pubmed_annotations? +

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.

What risk level is pdb_get_pubmed_annotations? +

pdb_get_pubmed_annotations is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit pdb_get_pubmed_annotations? +

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.

How do I block pdb_get_pubmed_annotations completely? +

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.

What MCP server provides pdb_get_pubmed_annotations? +

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.

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