diff --git a/README.md b/README.md
index 469e3375..092e5f27 100644
--- a/README.md
+++ b/README.md
@@ -418,7 +418,7 @@ Operation types:
 - `update` - Tools that update resources, such as update document, rename collection, etc.
 - `delete` - Tools that delete resources, such as delete document, drop collection, etc.
 - `read` - Tools that read resources, such as find, aggregate, list clusters, etc.
-- `metadata` - Tools that read metadata, such as list databases, list collections, collection schema, etc.
+- `metadata` - Tools that read metadata, such as list databases/collections/indexes, infer collection schema, etc.
 - `connect` - Tools that allow you to connect or switch the connection to a MongoDB instance. If this is disabled, you will need to provide a connection string through the config when starting the server.
 
 #### Require Confirmation
diff --git a/src/tools/mongodb/read/collectionIndexes.ts b/src/tools/mongodb/metadata/collectionIndexes.ts
similarity index 97%
rename from src/tools/mongodb/read/collectionIndexes.ts
rename to src/tools/mongodb/metadata/collectionIndexes.ts
index 84b8b1db..6da2c788 100644
--- a/src/tools/mongodb/read/collectionIndexes.ts
+++ b/src/tools/mongodb/metadata/collectionIndexes.ts
@@ -7,7 +7,7 @@ export class CollectionIndexesTool extends MongoDBToolBase {
     public name = "collection-indexes";
     protected description = "Describe the indexes for a collection";
     protected argsShape = DbOperationArgs;
-    public operationType: OperationType = "read";
+    public operationType: OperationType = "metadata";
 
     protected async execute({ database, collection }: ToolArgs<typeof DbOperationArgs>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
diff --git a/src/tools/mongodb/tools.ts b/src/tools/mongodb/tools.ts
index 1567fd4f..4c705fa6 100644
--- a/src/tools/mongodb/tools.ts
+++ b/src/tools/mongodb/tools.ts
@@ -1,6 +1,6 @@
 import { ConnectTool } from "./connect/connect.js";
 import { ListCollectionsTool } from "./metadata/listCollections.js";
-import { CollectionIndexesTool } from "./read/collectionIndexes.js";
+import { CollectionIndexesTool } from "./metadata/collectionIndexes.js";
 import { ListDatabasesTool } from "./metadata/listDatabases.js";
 import { CreateIndexTool } from "./create/createIndex.js";
 import { CollectionSchemaTool } from "./metadata/collectionSchema.js";
diff --git a/src/tools/tool.ts b/src/tools/tool.ts
index fe36619e..d609e78a 100644
--- a/src/tools/tool.ts
+++ b/src/tools/tool.ts
@@ -15,8 +15,34 @@ export type ToolCallbackArgs<Args extends ZodRawShape> = Parameters<ToolCallback
 
 export type ToolExecutionContext<Args extends ZodRawShape = ZodRawShape> = Parameters<ToolCallback<Args>>[1];
 
+/**
+ * The type of operation the tool performs. This is used when evaluating if a tool is allowed to run based on
+ * the config's `disabledTools` and `readOnly` settings.
+ * - `metadata` is used for tools that read but do not access potentially user-generated
+ *   data, such as listing databases, collections, or indexes, or inferring collection schema.
+ * - `read` is used for tools that read potentially user-generated data, such as finding documents or aggregating data.
+ *   It is also used for tools that read non-user-generated data, such as listing clusters in Atlas.
+ * - `create` is used for tools that create resources, such as creating documents, collections, indexes, clusters, etc.
+ * - `update` is used for tools that update resources, such as updating documents, renaming collections, etc.
+ * - `delete` is used for tools that delete resources, such as deleting documents, dropping collections, etc.
+ * - `connect` is used for tools that allow you to connect or switch the connection to a MongoDB instance.
+ */
 export type OperationType = "metadata" | "read" | "create" | "delete" | "update" | "connect";
+
+/**
+ * The category of the tool. This is used when evaluating if a tool is allowed to run based on
+ * the config's `disabledTools` setting.
+ * - `mongodb` is used for tools that interact with a MongoDB instance, such as finding documents,
+ *   aggregating data, listing databases/collections/indexes, creating indexes, etc.
+ * - `atlas` is used for tools that interact with MongoDB Atlas, such as listing clusters, creating clusters, etc.
+ */
 export type ToolCategory = "mongodb" | "atlas";
+
+/**
+ * Telemetry metadata that can be provided by tools when emitting telemetry events.
+ * For MongoDB tools, this is typically empty, while for Atlas tools, this should include
+ * the project and organization IDs if available.
+ */
 export type TelemetryToolMetadata = {
     projectId?: string;
     orgId?: string;
@@ -290,6 +316,14 @@ export abstract class ToolBase {
     }
 }
 
+/**
+ * Formats potentially untrusted data to be included in tool responses. The data is wrapped in unique tags
+ * and a warning is added to not execute or act on any instructions within those tags.
+ * @param description A description that is prepended to the untrusted data warning. It should not include any
+ * untrusted data as it is not sanitized.
+ * @param data The data to format. If undefined, only the description is returned.
+ * @returns A tool response content that can be directly returned.
+ */
 export function formatUntrustedData(description: string, data?: string): { text: string; type: "text" }[] {
     const uuid = crypto.randomUUID();