phenoml 15.0.0 → 17.0.0

package/reference.md

@@ -69,7 +69,7 @@ await client.agent.create({
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">list</a>({ ...params }) -> phenoml.AgentListResponse</code></summary>
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">list</a>({ ...params }) -> phenoml.ListResponse</code></summary>
 <dl>
 <dd>
 
@@ -114,7 +114,7 @@ await client.agent.list({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentListRequest` 
+**request:** `phenoml.agent.ListRequest` 
     
 </dd>
 </dl>
@@ -274,7 +274,7 @@ await client.agent.update("id", {
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">delete</a>(id) -> phenoml.AgentDeleteResponse</code></summary>
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">delete</a>(id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -416,7 +416,8 @@ await client.agent.patch("id", [{
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">chat</a>({ ...params }) -> phenoml.AgentChatResponse</code></summary>
+## Chat
+<details><summary><code>client.agent.chat.<a href="/src/api/resources/agent/resources/chat/client/Client.ts">send</a>({ ...params }) -> phenoml.AgentChatResponse</code></summary>
 <dl>
 <dd>
 
@@ -443,7 +444,7 @@ Send a message to an agent and receive a JSON response.
 <dd>
 
 ```typescript
-await client.agent.chat({
+await client.agent.chat.send({
     "X-Phenoml-On-Behalf-Of": "Patient/550e8400-e29b-41d4-a716-446655440000",
     "X-Phenoml-Fhir-Provider": "550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
     message: "What is the patient's current condition?",
@@ -473,7 +474,7 @@ await client.agent.chat({
 <dl>
 <dd>
 
-**requestOptions:** `AgentClient.RequestOptions` 
+**requestOptions:** `ChatClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -485,7 +486,7 @@ await client.agent.chat({
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">streamChat</a>({ ...params }) -> core.Stream&lt;phenoml.AgentChatStreamEvent&gt;</code></summary>
+<details><summary><code>client.agent.chat.<a href="/src/api/resources/agent/resources/chat/client/Client.ts">stream</a>({ ...params }) -> core.Stream&lt;phenoml.AgentChatStreamEvent&gt;</code></summary>
 <dl>
 <dd>
 
@@ -514,7 +515,7 @@ tool_result, message_end, and error.
 <dd>
 
 ```typescript
-const response = await client.agent.streamChat({
+const response = await client.agent.chat.stream({
     "X-Phenoml-On-Behalf-Of": "Patient/550e8400-e29b-41d4-a716-446655440000",
     "X-Phenoml-Fhir-Provider": "550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
     message: "What is the patient's current condition?",
@@ -547,7 +548,7 @@ for await (const item of response) {
 <dl>
 <dd>
 
-**requestOptions:** `AgentClient.RequestOptions` 
+**requestOptions:** `ChatClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -559,7 +560,7 @@ for await (const item of response) {
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">getChatMessages</a>({ ...params }) -> phenoml.AgentGetChatMessagesResponse</code></summary>
+<details><summary><code>client.agent.chat.<a href="/src/api/resources/agent/resources/chat/client/Client.ts">listMessages</a>({ ...params }) -> phenoml.ListMessagesResponse</code></summary>
 <dl>
 <dd>
 
@@ -586,7 +587,7 @@ Retrieves a list of chat messages for a given chat session
 <dd>
 
 ```typescript
-await client.agent.getChatMessages({
+await client.agent.chat.listMessages({
     chat_session_id: "chat_session_id",
     num_messages: 1,
     role: "user",
@@ -607,7 +608,7 @@ await client.agent.getChatMessages({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentGetChatMessagesRequest` 
+**request:** `phenoml.agent.ListMessagesRequest` 
     
 </dd>
 </dl>
@@ -615,7 +616,7 @@ await client.agent.getChatMessages({
 <dl>
 <dd>
 
-**requestOptions:** `AgentClient.RequestOptions` 
+**requestOptions:** `ChatClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1030,8 +1031,8 @@ await client.agent.prompts.patch("id", [{
 </dl>
 </details>
 
-## Authtoken Auth
-<details><summary><code>client.authtoken.auth.<a href="/src/api/resources/authtoken/resources/auth/client/Client.ts">getToken</a>({ ...params }) -> phenoml.TokenResponse</code></summary>
+## Authtoken
+<details><summary><code>client.authtoken.<a href="/src/api/resources/authtoken/client/Client.ts">getToken</a>({ ...params }) -> phenoml.TokenResponse</code></summary>
 <dl>
 <dd>
 
@@ -1061,7 +1062,7 @@ returns an access token with expiration information.
 <dd>
 
 ```typescript
-await client.authtoken.auth.getToken({
+await client.authtoken.getToken({
     client_id: "your_client_id",
     client_secret: "your_client_secret"
 });
@@ -1088,7 +1089,7 @@ await client.authtoken.auth.getToken({
 <dl>
 <dd>
 
-**requestOptions:** `AuthClient.RequestOptions` 
+**requestOptions:** `AuthtokenClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1167,7 +1168,7 @@ await client.cohort.analyze({
 </details>
 
 ## Construe
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">uploadCodeSystem</a>({ ...params }) -> phenoml.ConstrueUploadCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">submitFeedback</a>({ ...params }) -> phenoml.FeedbackResponse</code></summary>
 <dl>
 <dd>
 
@@ -1179,10 +1180,8 @@ await client.cohort.analyze({
 <dl>
 <dd>
 
-Upload a custom medical code system with codes and descriptions for use in code extraction. Requires a paid plan.
-Returns 202 immediately; embedding generation runs asynchronously. Poll
-GET /construe/codes/systems/{codesystem}?version={version} to check when status
-transitions from "processing" to "ready" or "failed".
+Submits user feedback on results from the Construe extraction endpoint.
+Feedback includes the full extraction result received and the result the user expected.
 </dd>
 </dl>
 </dd>
@@ -1197,17 +1196,31 @@ transitions from "processing" to "ready" or "failed".
 <dd>
 
 ```typescript
-await client.construe.uploadCodeSystem({
-    name: "CUSTOM_CODES",
-    version: "1.0",
-    format: "json",
-    codes: [{
-            code: "X001",
-            description: "Example custom code 1"
-        }, {
-            code: "X002",
-            description: "Example custom code 2"
-        }]
+await client.construe.submitFeedback({
+    text: "Patient has type 2 diabetes with hyperglycemia",
+    received_result: {
+        system: {
+            name: "ICD-10-CM",
+            version: "2025"
+        },
+        codes: [{
+                code: "E11.9",
+                description: "Type 2 diabetes mellitus without complications",
+                valid: true
+            }]
+    },
+    expected_result: {
+        system: {
+            name: "ICD-10-CM",
+            version: "2025"
+        },
+        codes: [{
+                code: "E11.65",
+                description: "Type 2 diabetes mellitus with hyperglycemia",
+                valid: true
+            }]
+    },
+    detail: "Expected code E11.65 because the text mentions hyperglycemia"
 });
 
 ```
@@ -1224,7 +1237,7 @@ await client.construe.uploadCodeSystem({
 <dl>
 <dd>
 
-**request:** `phenoml.construe.UploadRequest` 
+**request:** `phenoml.construe.FeedbackRequest` 
     
 </dd>
 </dl>
@@ -1244,7 +1257,8 @@ await client.construe.uploadCodeSystem({
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">extractCodes</a>({ ...params }) -> phenoml.ExtractCodesResult</code></summary>
+## Code Systems
+<details><summary><code>client.construe.codeSystems.<a href="/src/api/resources/construe/resources/codeSystems/client/Client.ts">upload</a>({ ...params }) -> phenoml.UploadResponse</code></summary>
 <dl>
 <dd>
 
@@ -1256,9 +1270,10 @@ await client.construe.uploadCodeSystem({
 <dl>
 <dd>
 
-Converts natural language text into structured medical codes.
-
-Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
+Upload a custom medical code system with codes and descriptions for use in code extraction. Requires a paid plan.
+Returns 202 immediately; embedding generation runs asynchronously. Poll
+GET /construe/codes/systems/{codesystem}?version={version} to check when status
+transitions from "processing" to "ready" or "failed".
 </dd>
 </dl>
 </dd>
@@ -1273,12 +1288,17 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.extractCodes({
-    text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
-    system: {
-        name: "ICD-10-CM",
-        version: "2025"
-    }
+await client.construe.codeSystems.upload({
+    name: "CUSTOM_CODES",
+    version: "1.0",
+    format: "json",
+    codes: [{
+            code: "X001",
+            description: "Example custom code 1"
+        }, {
+            code: "X002",
+            description: "Example custom code 2"
+        }]
 });
 
 ```
@@ -1295,7 +1315,7 @@ await client.construe.extractCodes({
 <dl>
 <dd>
 
-**request:** `phenoml.construe.ExtractRequest` 
+**request:** `phenoml.construe.UploadRequest` 
     
 </dd>
 </dl>
@@ -1303,7 +1323,7 @@ await client.construe.extractCodes({
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodeSystemsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1315,7 +1335,7 @@ await client.construe.extractCodes({
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listAvailableCodeSystems</a>() -> phenoml.ListCodeSystemsResponse</code></summary>
+<details><summary><code>client.construe.codeSystems.<a href="/src/api/resources/construe/resources/codeSystems/client/Client.ts">list</a>() -> phenoml.ListCodeSystemsResponse</code></summary>
 <dl>
 <dd>
 
@@ -1342,7 +1362,7 @@ Returns the terminology server's catalog of available code systems, including bo
 <dd>
 
 ```typescript
-await client.construe.listAvailableCodeSystems();
+await client.construe.codeSystems.list();
 
 ```
 </dd>
@@ -1358,7 +1378,7 @@ await client.construe.listAvailableCodeSystems();
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodeSystemsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1370,7 +1390,7 @@ await client.construe.listAvailableCodeSystems();
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getCodeSystemDetail</a>(codesystem, { ...params }) -> phenoml.GetCodeSystemDetailResponse</code></summary>
+<details><summary><code>client.construe.codeSystems.<a href="/src/api/resources/construe/resources/codeSystems/client/Client.ts">find</a>(codesystem, { ...params }) -> phenoml.GetCodeSystemDetailResponse</code></summary>
 <dl>
 <dd>
 
@@ -1397,7 +1417,7 @@ Returns full metadata for a single code system, including timestamps and builtin
 <dd>
 
 ```typescript
-await client.construe.getCodeSystemDetail("ICD-10-CM", {
+await client.construe.codeSystems.find("ICD-10-CM", {
     version: "2025"
 });
 
@@ -1423,7 +1443,7 @@ await client.construe.getCodeSystemDetail("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesSystemsCodesystemRequest` 
+**request:** `phenoml.construe.FindRequest` 
     
 </dd>
 </dl>
@@ -1431,7 +1451,7 @@ await client.construe.getCodeSystemDetail("ICD-10-CM", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodeSystemsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1443,7 +1463,7 @@ await client.construe.getCodeSystemDetail("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">deleteCustomCodeSystem</a>(codesystem, { ...params }) -> phenoml.DeleteCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.codeSystems.<a href="/src/api/resources/construe/resources/codeSystems/client/Client.ts">delete</a>(codesystem, { ...params }) -> phenoml.DeleteCodeSystemResponse</code></summary>
 <dl>
 <dd>
 
@@ -1471,7 +1491,7 @@ Only available on dedicated instances. Large systems may take up to a minute to
 <dd>
 
 ```typescript
-await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
+await client.construe.codeSystems.delete("CUSTOM_CODES", {
     version: "version"
 });
 
@@ -1497,7 +1517,7 @@ await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.DeleteConstrueCodesSystemsCodesystemRequest` 
+**request:** `phenoml.construe.DeleteRequest` 
     
 </dd>
 </dl>
@@ -1505,7 +1525,7 @@ await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodeSystemsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1517,7 +1537,7 @@ await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">exportCustomCodeSystem</a>(codesystem, { ...params }) -> phenoml.ExportCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.codeSystems.<a href="/src/api/resources/construe/resources/codeSystems/client/Client.ts">export</a>(codesystem, { ...params }) -> phenoml.ExportCodeSystemResponse</code></summary>
 <dl>
 <dd>
 
@@ -1546,7 +1566,7 @@ Only available on dedicated instances. Builtin systems cannot be exported.
 <dd>
 
 ```typescript
-await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
+await client.construe.codeSystems.export("CUSTOM_CODES", {
     version: "version"
 });
 
@@ -1572,7 +1592,7 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesSystemsCodesystemExportRequest` 
+**request:** `phenoml.construe.ExportRequest` 
     
 </dd>
 </dl>
@@ -1580,7 +1600,7 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodeSystemsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1592,7 +1612,8 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listCodesInACodeSystem</a>(codesystem, { ...params }) -> phenoml.ListCodesResponse</code></summary>
+## Codes
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">extract</a>({ ...params }) -> phenoml.ExtractCodesResult</code></summary>
 <dl>
 <dd>
 
@@ -1604,7 +1625,7 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-Returns a paginated list of all codes in the specified code system from the terminology server.
+Converts natural language text into structured medical codes.
 
 Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 </dd>
@@ -1621,10 +1642,12 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.listCodesInACodeSystem("ICD-10-CM", {
-    version: "2025",
-    cursor: "cursor",
-    limit: 1
+await client.construe.codes.extract({
+    text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
+    system: {
+        name: "ICD-10-CM",
+        version: "2025"
+    }
 });
 
 ```
@@ -1641,15 +1664,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 <dl>
 <dd>
 
-**codesystem:** `string` — Code system name (e.g., "ICD-10-CM", "SNOMED_CT_US_LITE")
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**request:** `phenoml.construe.GetConstrueCodesCodesystemRequest` 
+**request:** `phenoml.construe.ExtractRequest` 
     
 </dd>
 </dl>
@@ -1657,7 +1672,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1669,7 +1684,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getASpecificCode</a>(codesystem, codeID, { ...params }) -> phenoml.GetCodeResponse</code></summary>
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">list</a>(codesystem, { ...params }) -> phenoml.ListCodesResponse</code></summary>
 <dl>
 <dd>
 
@@ -1681,7 +1696,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 <dl>
 <dd>
 
-Looks up a specific code in the terminology server and returns its details.
+Returns a paginated list of all codes in the specified code system from the terminology server.
 
 Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 </dd>
@@ -1698,8 +1713,10 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.getASpecificCode("ICD-10-CM", "E1165", {
-    version: "version"
+await client.construe.codes.list("ICD-10-CM", {
+    version: "2025",
+    cursor: "cursor",
+    limit: 1
 });
 
 ```
@@ -1716,18 +1733,7 @@ await client.construe.getASpecificCode("ICD-10-CM", "E1165", {
 <dl>
 <dd>
 
-**codesystem:** `string` — Code system name
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**codeID:** `string` 
-
-The code identifier. ICD-10-CM codes are stored without their
-cosmetic dot (use "E1165", not "E11.65").
+**codesystem:** `string` — Code system name (e.g., "ICD-10-CM", "SNOMED_CT_US_LITE")
     
 </dd>
 </dl>
@@ -1735,7 +1741,7 @@ cosmetic dot (use "E1165", not "E11.65").
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemCodeIdRequest` 
+**request:** `phenoml.construe.CodesListRequest` 
     
 </dd>
 </dl>
@@ -1743,7 +1749,7 @@ cosmetic dot (use "E1165", not "E11.65").
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1755,7 +1761,7 @@ cosmetic dot (use "E1165", not "E11.65").
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">semanticSearchEmbeddingBased</a>(codesystem, { ...params }) -> phenoml.SemanticSearchResponse</code></summary>
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">lookup</a>(codesystem, codeID, { ...params }) -> phenoml.GetCodeResponse</code></summary>
 <dl>
 <dd>
 
@@ -1767,23 +1773,7 @@ cosmetic dot (use "E1165", not "E11.65").
 <dl>
 <dd>
 
-Performs semantic similarity search using vector embeddings.
-
-**Availability**: This endpoint works for both **built-in and custom** code systems.
-
-**When to use**: Best for natural language queries where you want to find conceptually
-related codes, even when different terminology is used. The search understands meaning,
-not just keywords.
-
-**Examples**:
-- Query "trouble breathing at night" finds codes like "Sleep apnea", "Orthopnea",
-  "Nocturnal dyspnea" — semantically related but no exact keyword matches
-- Query "heart problems" finds "Myocardial infarction", "Cardiac arrest", "Arrhythmia"
-
-**Trade-offs**: Slower than text search (requires embedding generation), but finds
-conceptually similar results that keyword search would miss.
-
-See also: `/search/text` for faster keyword-based lookup with typo tolerance.
+Looks up a specific code in the terminology server and returns its details.
 
 Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 </dd>
@@ -1800,10 +1790,8 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
-    text: "patient has trouble breathing at night and wakes up gasping",
-    version: "version",
-    limit: 1
+await client.construe.codes.lookup("ICD-10-CM", "E1165", {
+    version: "version"
 });
 
 ```
@@ -1828,7 +1816,10 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemSearchSemanticRequest` 
+**codeID:** `string` 
+
+The code identifier. ICD-10-CM codes are stored without their
+cosmetic dot (use "E1165", not "E11.65").
     
 </dd>
 </dl>
@@ -1836,7 +1827,15 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**request:** `phenoml.construe.LookupRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `CodesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1848,7 +1847,7 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">submitFeedbackOnExtractionResults</a>({ ...params }) -> phenoml.FeedbackResponse</code></summary>
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">searchSemantic</a>(codesystem, { ...params }) -> phenoml.SemanticSearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -1860,8 +1859,25 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 <dl>
 <dd>
 
-Submits user feedback on results from the Construe extraction endpoint.
-Feedback includes the full extraction result received and the result the user expected.
+Performs semantic similarity search using vector embeddings.
+
+**Availability**: This endpoint works for both **built-in and custom** code systems.
+
+**When to use**: Best for natural language queries where you want to find conceptually
+related codes, even when different terminology is used. The search understands meaning,
+not just keywords.
+
+**Examples**:
+- Query "trouble breathing at night" finds codes like "Sleep apnea", "Orthopnea",
+  "Nocturnal dyspnea" — semantically related but no exact keyword matches
+- Query "heart problems" finds "Myocardial infarction", "Cardiac arrest", "Arrhythmia"
+
+**Trade-offs**: Slower than text search (requires embedding generation), but finds
+conceptually similar results that keyword search would miss.
+
+See also: `/search/text` for faster keyword-based lookup with typo tolerance.
+
+Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 </dd>
 </dl>
 </dd>
@@ -1876,31 +1892,10 @@ Feedback includes the full extraction result received and the result the user ex
 <dd>
 
 ```typescript
-await client.construe.submitFeedbackOnExtractionResults({
-    text: "Patient has type 2 diabetes with hyperglycemia",
-    received_result: {
-        system: {
-            name: "ICD-10-CM",
-            version: "2025"
-        },
-        codes: [{
-                code: "E11.9",
-                description: "Type 2 diabetes mellitus without complications",
-                valid: true
-            }]
-    },
-    expected_result: {
-        system: {
-            name: "ICD-10-CM",
-            version: "2025"
-        },
-        codes: [{
-                code: "E11.65",
-                description: "Type 2 diabetes mellitus with hyperglycemia",
-                valid: true
-            }]
-    },
-    detail: "Expected code E11.65 because the text mentions hyperglycemia"
+await client.construe.codes.searchSemantic("ICD-10-CM", {
+    text: "patient has trouble breathing at night and wakes up gasping",
+    version: "version",
+    limit: 1
 });
 
 ```
@@ -1917,7 +1912,7 @@ await client.construe.submitFeedbackOnExtractionResults({
 <dl>
 <dd>
 
-**request:** `phenoml.construe.FeedbackRequest` 
+**codesystem:** `string` — Code system name
     
 </dd>
 </dl>
@@ -1925,7 +1920,15 @@ await client.construe.submitFeedbackOnExtractionResults({
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**request:** `phenoml.construe.SearchSemanticRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `CodesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1937,7 +1940,7 @@ await client.construe.submitFeedbackOnExtractionResults({
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">terminologyServerTextSearch</a>(codesystem, { ...params }) -> phenoml.TextSearchResponse</code></summary>
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">searchText</a>(codesystem, { ...params }) -> phenoml.TextSearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -1987,7 +1990,7 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.terminologyServerTextSearch("ICD-10-CM", {
+await client.construe.codes.searchText("ICD-10-CM", {
     q: "E11.65",
     version: "version",
     limit: 1
@@ -2015,7 +2018,7 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemSearchTextRequest` 
+**request:** `phenoml.construe.SearchTextRequest` 
     
 </dd>
 </dl>
@@ -2023,7 +2026,7 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 <dl>
 <dd>
 
-**requestOptions:** `ConstrueClient.RequestOptions` 
+**requestOptions:** `CodesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -2036,7 +2039,7 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 </details>
 
 ## Fhir
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">search</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.FhirSearchResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">search</a>(fhir_provider_id, fhir_path, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2048,7 +2051,19 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 <dl>
 <dd>
 
-Retrieves FHIR resources from the specified provider. Supports both individual resource retrieval and search operations based on the FHIR path and query parameters.
+Retrieves FHIR resources from the specified provider. Supports both individual resource retrieval (e.g. `Patient/123` via the path) and search operations.
+
+FHIR search parameters are passed through to the upstream server verbatim as native query-string parameters; this proxy does not model, validate, or transform them. Append standard FHIR search parameters directly to the request URL. Supported parameters include:
+- Resource-specific search parameters (e.g. `name` for Patient, `status` for Observation)
+- Common search parameters (`_id`, `_lastUpdated`, `_tag`, `_profile`, `_security`, `_text`, `_content`, `_filter`)
+- Result parameters (`_count`, `_offset`, `_sort`, `_include`, `_revinclude`, `_summary`, `_elements`)
+- Search prefixes for dates, numbers, and quantities (`eq`, `ne`, `gt`, `ge`, `lt`, `le`, `sa`, `eb`, `ap`)
+
+Examples:
+- `Patient?name=John%20Doe&_count=10&_sort=family`
+- `Observation?patient=Patient/123&date=ge2023-01-01&category=vital-signs&_sort=-date`
+
+When using a generated SDK, supply these via the client's request-level query-parameter option (the SDK escape hatch) rather than a typed argument.
 
 The request is proxied to the configured FHIR server with appropriate authentication headers.
 </dd>
@@ -2110,7 +2125,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirSearchRequest` 
+**request:** `phenoml.fhir.SearchRequest` 
     
 </dd>
 </dl>
@@ -2130,7 +2145,7 @@ Examples:
 </dl>
 </details>
 
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">create</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">create</a>(fhir_provider_id, fhir_path, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2163,7 +2178,7 @@ await client.fhir.create("550e8400-e29b-41d4-a716-446655440000", "Patient", {
     "X-Phenoml-On-Behalf-Of": "Patient/550e8400-e29b-41d4-a716-446655440000",
     "X-Phenoml-Fhir-Provider": "550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
     body: {
-        resourceType: "Patient"
+        "resourceType": "Patient"
     }
 });
 
@@ -2207,7 +2222,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirCreateRequest` 
+**request:** `phenoml.fhir.CreateRequest` 
     
 </dd>
 </dl>
@@ -2227,7 +2242,7 @@ Examples:
 </dl>
 </details>
 
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">upsert</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">upsert</a>(fhir_provider_id, fhir_path, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2260,8 +2275,8 @@ await client.fhir.upsert("550e8400-e29b-41d4-a716-446655440000", "Patient", {
     "X-Phenoml-On-Behalf-Of": "Patient/550e8400-e29b-41d4-a716-446655440000",
     "X-Phenoml-Fhir-Provider": "550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
     body: {
-        resourceType: "Patient",
-        id: "123"
+        "resourceType": "Patient",
+        "id": "123"
     }
 });
 
@@ -2305,7 +2320,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirUpsertRequest` 
+**request:** `phenoml.fhir.UpsertRequest` 
     
 </dd>
 </dl>
@@ -2325,7 +2340,7 @@ Examples:
 </dl>
 </details>
 
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">delete</a>(fhir_provider_id, fhir_path, { ...params }) -> Record&lt;string, unknown&gt;</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">delete</a>(fhir_provider_id, fhir_path, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2399,7 +2414,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirDeleteRequest` 
+**request:** `phenoml.fhir.DeleteRequest` 
     
 </dd>
 </dl>
@@ -2419,7 +2434,7 @@ Examples:
 </dl>
 </details>
 
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">patch</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">patch</a>(fhir_provider_id, fhir_path, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2431,12 +2446,16 @@ Examples:
 <dl>
 <dd>
 
-Partially updates a FHIR resource on the specified provider using JSON Patch operations as defined in RFC 6902.
+Partially updates a FHIR resource on the specified provider.
+
+Two body formats are supported, selected by request content type:
+- `application/json-patch+json` — an array of JSON Patch operations as defined in RFC 6902. Each operation specifies:
+  - `op`: The operation type (add, remove, replace, move, copy, test)
+  - `path`: JSON Pointer to the target location in the resource
+  - `value`: The value to use (required for add, replace, and test operations)
+- `application/fhir+json` — a partial FHIR resource for merge-patch semantics.
 
-The request body should contain an array of JSON Patch operations. Each operation specifies:
-- `op`: The operation type (add, remove, replace, move, copy, test)
-- `path`: JSON Pointer to the target location in the resource
-- `value`: The value to use (required for add, replace, and test operations)
+**Note:** This proxy currently forwards the request body to the upstream FHIR server with `Content-Type: application/fhir+json` regardless of the declared request content type. JSON Patch (RFC 6902) therefore only succeeds against upstream servers that accept patch arrays under `application/fhir+json`; servers that strictly enforce patch media types may reject or misinterpret it. Support for either format ultimately depends on the upstream FHIR server.
 
 The request is proxied to the configured FHIR server with appropriate authentication headers.
 </dd>
@@ -2503,7 +2522,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirPatchRequest` 
+**request:** `phenoml.fhir.PatchRequest` 
     
 </dd>
 </dl>
@@ -2523,7 +2542,7 @@ Examples:
 </dl>
 </details>
 
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">executeBundle</a>(fhir_provider_id, { ...params }) -> phenoml.FhirBundle</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">executeBundle</a>(fhir_provider_id, { ...params }) -> unknown</code></summary>
 <dl>
 <dd>
 
@@ -2558,9 +2577,15 @@ await client.fhir.executeBundle("550e8400-e29b-41d4-a716-446655440000", {
     "X-Phenoml-On-Behalf-Of": "Patient/550e8400-e29b-41d4-a716-446655440000",
     "X-Phenoml-Fhir-Provider": "550e8400-e29b-41d4-a716-446655440000:eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c...",
     body: {
-        resourceType: "Bundle",
-        entry: [{
-                resource: {
+        "resourceType": "Bundle",
+        "type": "transaction",
+        "entry": [
+            {
+                "request": {
+                    "method": "POST",
+                    "url": "Patient"
+                },
+                "resource": {
                     "resourceType": "Patient",
                     "name": [
                         {
@@ -2570,24 +2595,22 @@ await client.fhir.executeBundle("550e8400-e29b-41d4-a716-446655440000", {
                             ]
                         }
                     ]
-                },
-                request: {
-                    method: "POST",
-                    url: "Patient"
                 }
-            }, {
-                resource: {
+            },
+            {
+                "request": {
+                    "method": "POST",
+                    "url": "Observation"
+                },
+                "resource": {
                     "resourceType": "Observation",
                     "status": "final",
                     "subject": {
                         "reference": "Patient/123"
                     }
-                },
-                request: {
-                    method: "POST",
-                    url: "Observation"
                 }
-            }]
+            }
+        ]
     }
 });
 
@@ -2617,7 +2640,7 @@ The ID of the FHIR provider to use. Can be either:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirExecuteBundleRequest` 
+**request:** `phenoml.fhir.ExecuteBundleRequest` 
     
 </dd>
 </dl>
@@ -2837,7 +2860,7 @@ await client.fhirProvider.get("fhir_provider_id");
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhir_provider_id) -> phenoml.FhirProviderDeleteResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhir_provider_id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -2902,7 +2925,8 @@ await client.fhirProvider.delete("fhir_provider_id");
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">addAuthConfig</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
+## Auth Config
+<details><summary><code>client.fhirProvider.authConfig.<a href="/src/api/resources/fhirProvider/resources/authConfig/client/Client.ts">add</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
 <dl>
 <dd>
 
@@ -2932,7 +2956,7 @@ Note: Sandbox providers cannot be modified.
 <dd>
 
 ```typescript
-await client.fhirProvider.addAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+await client.fhirProvider.authConfig.add("1716d214-de93-43a4-aa6b-a878d864e2ad", {
     auth_method: "client_secret",
     client_id: "your-client-id",
     client_secret: "your-client-secret"
@@ -2968,7 +2992,7 @@ await client.fhirProvider.addAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad",
 <dl>
 <dd>
 
-**requestOptions:** `FhirProviderClient.RequestOptions` 
+**requestOptions:** `AuthConfigClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -2980,7 +3004,7 @@ await client.fhirProvider.addAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad",
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">setActiveAuthConfig</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
+<details><summary><code>client.fhirProvider.authConfig.<a href="/src/api/resources/fhirProvider/resources/authConfig/client/Client.ts">setActive</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
 <dl>
 <dd>
 
@@ -3013,7 +3037,7 @@ Note: Sandbox providers cannot be modified.
 <dd>
 
 ```typescript
-await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+await client.fhirProvider.authConfig.setActive("1716d214-de93-43a4-aa6b-a878d864e2ad", {
     auth_config_id: "auth-config-456"
 });
 
@@ -3047,7 +3071,7 @@ await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e
 <dl>
 <dd>
 
-**requestOptions:** `FhirProviderClient.RequestOptions` 
+**requestOptions:** `AuthConfigClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3059,7 +3083,7 @@ await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">removeAuthConfig</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderRemoveAuthConfigResponse</code></summary>
+<details><summary><code>client.fhirProvider.authConfig.<a href="/src/api/resources/fhirProvider/resources/authConfig/client/Client.ts">remove</a>(fhir_provider_id, { ...params }) -> phenoml.RemoveResponse</code></summary>
 <dl>
 <dd>
 
@@ -3089,7 +3113,7 @@ Note: Sandbox providers cannot be modified.
 <dd>
 
 ```typescript
-await client.fhirProvider.removeAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+await client.fhirProvider.authConfig.remove("1716d214-de93-43a4-aa6b-a878d864e2ad", {
     auth_config_id: "auth-config-456"
 });
 
@@ -3123,7 +3147,7 @@ await client.fhirProvider.removeAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad
 <dl>
 <dd>
 
-**requestOptions:** `FhirProviderClient.RequestOptions` 
+**requestOptions:** `AuthConfigClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3347,7 +3371,7 @@ await client.lang2Fhir.search({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.Lang2FhirUploadProfileResponse</code></summary>
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.UploadProfileResponse</code></summary>
 <dl>
 <dd>
 
@@ -3492,7 +3516,7 @@ await client.lang2Fhir.document({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">extractMultipleFhirResourcesFromADocument</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">documentMulti</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
 <dl>
 <dd>
 
@@ -3524,7 +3548,7 @@ Resources are linked with proper references (e.g., Conditions reference the Pati
 <dd>
 
 ```typescript
-await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
+await client.lang2Fhir.documentMulti({
     version: "R4",
     content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)",
     provider: "medplum"
@@ -3565,7 +3589,7 @@ await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
 </details>
 
 ## Summary
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">listTemplates</a>() -> phenoml.SummaryListTemplatesResponse</code></summary>
+<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryResponse</code></summary>
 <dl>
 <dd>
 
@@ -3577,7 +3601,10 @@ await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
 <dl>
 <dd>
 
-Retrieves all summary templates for the authenticated user
+Creates a summary from FHIR resources using one of three modes:
+- **narrative**: Uses a template to substitute FHIR data into placeholders (requires template_id)
+- **flatten**: Flattens FHIR resources into a searchable format for RAG/search (no template needed)
+- **ips**: Generates an International Patient Summary (IPS) narrative per ISO 27269/HL7 FHIR IPS IG. Requires a Bundle with exactly one Patient resource (returns 400 error if no Patient or multiple Patients are present). Automatically filters resources to those referencing the patient and generates sections for allergies, medications, problems, immunizations, procedures, and vital signs.
 </dd>
 </dl>
 </dd>
@@ -3592,7 +3619,40 @@ Retrieves all summary templates for the authenticated user
 <dd>
 
 ```typescript
-await client.summary.listTemplates();
+await client.summary.create({
+    mode: "narrative",
+    template_id: "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
+    fhir_resources: {
+        "resourceType": "Bundle",
+        "type": "collection",
+        "entry": [
+            {
+                "resource": {
+                    "resourceType": "Patient",
+                    "name": [
+                        {
+                            "given": [
+                                "John"
+                            ],
+                            "family": "Doe"
+                        }
+                    ],
+                    "gender": "male",
+                    "birthDate": "1979-03-15"
+                }
+            },
+            {
+                "resource": {
+                    "resourceType": "Condition",
+                    "code": {
+                        "text": "Type 2 Diabetes Mellitus"
+                    },
+                    "onsetDateTime": "2024-01-15"
+                }
+            }
+        ]
+    }
+});
 
 ```
 </dd>
@@ -3608,6 +3668,14 @@ await client.summary.listTemplates();
 <dl>
 <dd>
 
+**request:** `phenoml.summary.CreateSummaryRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
 **requestOptions:** `SummaryClient.RequestOptions` 
     
 </dd>
@@ -3620,7 +3688,8 @@ await client.summary.listTemplates();
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">createTemplate</a>({ ...params }) -> phenoml.CreateSummaryTemplateResponse</code></summary>
+## Templates
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">list</a>() -> phenoml.ListResponse</code></summary>
 <dl>
 <dd>
 
@@ -3632,7 +3701,7 @@ await client.summary.listTemplates();
 <dl>
 <dd>
 
-Creates a summary template from an example using LLM function calling
+Retrieves all summary templates for the authenticated user
 </dd>
 </dl>
 </dd>
@@ -3647,12 +3716,7 @@ Creates a summary template from an example using LLM function calling
 <dd>
 
 ```typescript
-await client.summary.createTemplate({
-    name: "Discharge Summary",
-    example_summary: "Patient John Doe, age 45, was admitted on 2024-01-10 with Type 2 Diabetes. Discharged on 2024-01-15 with Metformin 500mg BID.",
-    target_resources: ["Patient", "Condition", "MedicationRequest"],
-    mode: "narrative"
-});
+await client.summary.templates.list();
 
 ```
 </dd>
@@ -3668,15 +3732,7 @@ await client.summary.createTemplate({
 <dl>
 <dd>
 
-**request:** `phenoml.summary.CreateSummaryTemplateRequest` 
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3688,7 +3744,7 @@ await client.summary.createTemplate({
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">getTemplate</a>(id) -> phenoml.SummaryGetTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryTemplateResponse</code></summary>
 <dl>
 <dd>
 
@@ -3700,7 +3756,7 @@ await client.summary.createTemplate({
 <dl>
 <dd>
 
-Retrieves a specific summary template
+Creates a summary template from an example using LLM function calling
 </dd>
 </dl>
 </dd>
@@ -3715,7 +3771,12 @@ Retrieves a specific summary template
 <dd>
 
 ```typescript
-await client.summary.getTemplate("id");
+await client.summary.templates.create({
+    name: "Discharge Summary",
+    example_summary: "Patient John Doe, age 45, was admitted on 2024-01-10 with Type 2 Diabetes. Discharged on 2024-01-15 with Metformin 500mg BID.",
+    target_resources: ["Patient", "Condition", "MedicationRequest"],
+    mode: "narrative"
+});
 
 ```
 </dd>
@@ -3731,7 +3792,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-**id:** `string` — Template ID
+**request:** `phenoml.summary.CreateSummaryTemplateRequest` 
     
 </dd>
 </dl>
@@ -3739,7 +3800,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3751,7 +3812,7 @@ await client.summary.getTemplate("id");
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">updateTemplate</a>(id, { ...params }) -> phenoml.SummaryUpdateTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">get</a>(id) -> phenoml.GetResponse</code></summary>
 <dl>
 <dd>
 
@@ -3763,7 +3824,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-Updates an existing summary template
+Retrieves a specific summary template
 </dd>
 </dl>
 </dd>
@@ -3778,12 +3839,7 @@ Updates an existing summary template
 <dd>
 
 ```typescript
-await client.summary.updateTemplate("id", {
-    name: "Discharge Summary",
-    template: "Patient {{Patient.name[0].text}} was discharged on {{Encounter[0].period.end}} with {{MedicationRequest[0].medicationCodeableConcept.coding[0].display}} {{MedicationRequest[0].dosageInstruction[0].text}}.",
-    target_resources: ["Patient", "Encounter", "MedicationRequest"],
-    mode: "narrative"
-});
+await client.summary.templates.get("id");
 
 ```
 </dd>
@@ -3807,15 +3863,7 @@ await client.summary.updateTemplate("id", {
 <dl>
 <dd>
 
-**request:** `phenoml.summary.UpdateSummaryTemplateRequest` 
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3827,7 +3875,7 @@ await client.summary.updateTemplate("id", {
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">deleteTemplate</a>(id) -> phenoml.SummaryDeleteTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">update</a>(id, { ...params }) -> phenoml.UpdateResponse</code></summary>
 <dl>
 <dd>
 
@@ -3839,7 +3887,7 @@ await client.summary.updateTemplate("id", {
 <dl>
 <dd>
 
-Deletes a summary template
+Updates an existing summary template
 </dd>
 </dl>
 </dd>
@@ -3854,7 +3902,12 @@ Deletes a summary template
 <dd>
 
 ```typescript
-await client.summary.deleteTemplate("id");
+await client.summary.templates.update("id", {
+    name: "Discharge Summary",
+    template: "Patient {{Patient.name[0].text}} was discharged on {{Encounter[0].period.end}} with {{MedicationRequest[0].medicationCodeableConcept.coding[0].display}} {{MedicationRequest[0].dosageInstruction[0].text}}.",
+    target_resources: ["Patient", "Encounter", "MedicationRequest"],
+    mode: "narrative"
+});
 
 ```
 </dd>
@@ -3878,7 +3931,15 @@ await client.summary.deleteTemplate("id");
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**request:** `phenoml.summary.UpdateSummaryTemplateRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3890,7 +3951,7 @@ await client.summary.deleteTemplate("id");
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">delete</a>(id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -3902,10 +3963,7 @@ await client.summary.deleteTemplate("id");
 <dl>
 <dd>
 
-Creates a summary from FHIR resources using one of three modes:
-- **narrative**: Uses a template to substitute FHIR data into placeholders (requires template_id)
-- **flatten**: Flattens FHIR resources into a searchable format for RAG/search (no template needed)
-- **ips**: Generates an International Patient Summary (IPS) narrative per ISO 27269/HL7 FHIR IPS IG. Requires a Bundle with exactly one Patient resource (returns 400 error if no Patient or multiple Patients are present). Automatically filters resources to those referencing the patient and generates sections for allergies, medications, problems, immunizations, procedures, and vital signs.
+Deletes a summary template
 </dd>
 </dl>
 </dd>
@@ -3920,40 +3978,7 @@ Creates a summary from FHIR resources using one of three modes:
 <dd>
 
 ```typescript
-await client.summary.create({
-    mode: "narrative",
-    template_id: "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
-    fhir_resources: {
-        "resourceType": "Bundle",
-        "type": "collection",
-        "entry": [
-            {
-                "resource": {
-                    "resourceType": "Patient",
-                    "name": [
-                        {
-                            "given": [
-                                "John"
-                            ],
-                            "family": "Doe"
-                        }
-                    ],
-                    "gender": "male",
-                    "birthDate": "1979-03-15"
-                }
-            },
-            {
-                "resource": {
-                    "resourceType": "Condition",
-                    "code": {
-                        "text": "Type 2 Diabetes Mellitus"
-                    },
-                    "onsetDateTime": "2024-01-15"
-                }
-            }
-        ]
-    }
-});
+await client.summary.templates.delete("id");
 
 ```
 </dd>
@@ -3969,7 +3994,7 @@ await client.summary.create({
 <dl>
 <dd>
 
-**request:** `phenoml.summary.CreateSummaryRequest` 
+**id:** `string` — Template ID
     
 </dd>
 </dl>
@@ -3977,7 +4002,7 @@ await client.summary.create({
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4269,8 +4294,8 @@ await client.tools.analyzeCohort({
 </dl>
 </details>
 
-## Tools McpServer
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">create</a>({ ...params }) -> phenoml.McpServerResponse</code></summary>
+## MCP Servers
+<details><summary><code>client.tools.mcpServers.<a href="/src/api/resources/tools/resources/mcpServers/client/Client.ts">create</a>({ ...params }) -> phenoml.McpServerResponse</code></summary>
 <dl>
 <dd>
 
@@ -4297,7 +4322,7 @@ Creates a new MCP server
 <dd>
 
 ```typescript
-await client.tools.mcpServer.create({
+await client.tools.mcpServers.create({
     name: "My MCP Server",
     mcp_server_url: "https://mcp.example.com"
 });
@@ -4324,7 +4349,7 @@ await client.tools.mcpServer.create({
 <dl>
 <dd>
 
-**requestOptions:** `McpServerClient.RequestOptions` 
+**requestOptions:** `McpServersClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4336,7 +4361,7 @@ await client.tools.mcpServer.create({
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">list</a>() -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.tools.mcpServers.<a href="/src/api/resources/tools/resources/mcpServers/client/Client.ts">list</a>() -> phenoml.McpServerResponse</code></summary>
 <dl>
 <dd>
 
@@ -4363,7 +4388,7 @@ Lists all MCP servers for a specific user
 <dd>
 
 ```typescript
-await client.tools.mcpServer.list();
+await client.tools.mcpServers.list();
 
 ```
 </dd>
@@ -4379,7 +4404,7 @@ await client.tools.mcpServer.list();
 <dl>
 <dd>
 
-**requestOptions:** `McpServerClient.RequestOptions` 
+**requestOptions:** `McpServersClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4391,7 +4416,7 @@ await client.tools.mcpServer.list();
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">get</a>(mcp_server_id) -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.tools.mcpServers.<a href="/src/api/resources/tools/resources/mcpServers/client/Client.ts">get</a>(mcp_server_id) -> phenoml.McpServerResponse</code></summary>
 <dl>
 <dd>
 
@@ -4418,7 +4443,7 @@ Gets a MCP server by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.get("mcp_server_id");
+await client.tools.mcpServers.get("mcp_server_id");
 
 ```
 </dd>
@@ -4442,7 +4467,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `McpServerClient.RequestOptions` 
+**requestOptions:** `McpServersClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4454,7 +4479,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">delete</a>(mcp_server_id) -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.tools.mcpServers.<a href="/src/api/resources/tools/resources/mcpServers/client/Client.ts">delete</a>(mcp_server_id) -> phenoml.McpServerResponse</code></summary>
 <dl>
 <dd>
 
@@ -4481,7 +4506,7 @@ Deletes a MCP server by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.delete("mcp_server_id");
+await client.tools.mcpServers.delete("mcp_server_id");
 
 ```
 </dd>
@@ -4505,7 +4530,7 @@ await client.tools.mcpServer.delete("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `McpServerClient.RequestOptions` 
+**requestOptions:** `McpServersClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4517,8 +4542,8 @@ await client.tools.mcpServer.delete("mcp_server_id");
 </dl>
 </details>
 
-## Tools McpServer Tools
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">list</a>(mcp_server_id) -> phenoml.McpServerToolResponse</code></summary>
+## Tools McpTools
+<details><summary><code>client.tools.mcpTools.<a href="/src/api/resources/tools/resources/mcpTools/client/Client.ts">list</a>(mcp_server_id) -> phenoml.McpServerToolResponse</code></summary>
 <dl>
 <dd>
 
@@ -4545,7 +4570,7 @@ Lists all MCP server tools for a specific MCP server
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.list("mcp_server_id");
+await client.tools.mcpTools.list("mcp_server_id");
 
 ```
 </dd>
@@ -4569,7 +4594,7 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `ToolsClient.RequestOptions` 
+**requestOptions:** `McpToolsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4581,7 +4606,7 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">get</a>(mcp_server_tool_id) -> phenoml.McpServerToolResponse</code></summary>
+<details><summary><code>client.tools.mcpTools.<a href="/src/api/resources/tools/resources/mcpTools/client/Client.ts">get</a>(mcp_server_tool_id) -> phenoml.McpServerToolResponse</code></summary>
 <dl>
 <dd>
 
@@ -4608,7 +4633,7 @@ Gets a MCP server tool by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.get("mcp_server_tool_id");
+await client.tools.mcpTools.get("mcp_server_tool_id");
 
 ```
 </dd>
@@ -4632,7 +4657,7 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 <dl>
 <dd>
 
-**requestOptions:** `ToolsClient.RequestOptions` 
+**requestOptions:** `McpToolsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4644,7 +4669,7 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">delete</a>(mcp_server_tool_id) -> phenoml.McpServerToolResponse</code></summary>
+<details><summary><code>client.tools.mcpTools.<a href="/src/api/resources/tools/resources/mcpTools/client/Client.ts">delete</a>(mcp_server_tool_id) -> phenoml.McpServerToolResponse</code></summary>
 <dl>
 <dd>
 
@@ -4671,7 +4696,7 @@ Deletes a MCP server tool by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
+await client.tools.mcpTools.delete("mcp_server_tool_id");
 
 ```
 </dd>
@@ -4695,7 +4720,7 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 <dl>
 <dd>
 
-**requestOptions:** `ToolsClient.RequestOptions` 
+**requestOptions:** `McpToolsClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4753,7 +4778,7 @@ await client.workflows.list({
 <dl>
 <dd>
 
-**request:** `phenoml.workflows.WorkflowsListRequest` 
+**request:** `phenoml.workflows.ListRequest` 
     
 </dd>
 </dl>
@@ -4847,7 +4872,7 @@ await client.workflows.create({
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">get</a>(id, { ...params }) -> phenoml.WorkflowsGetResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">get</a>(id, { ...params }) -> phenoml.GetResponse</code></summary>
 <dl>
 <dd>
 
@@ -4900,7 +4925,7 @@ await client.workflows.get("id", {
 <dl>
 <dd>
 
-**request:** `phenoml.workflows.WorkflowsGetRequest` 
+**request:** `phenoml.workflows.GetRequest` 
     
 </dd>
 </dl>
@@ -4920,7 +4945,7 @@ await client.workflows.get("id", {
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">update</a>(id, { ...params }) -> phenoml.WorkflowsUpdateResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">update</a>(id, { ...params }) -> phenoml.UpdateResponse</code></summary>
 <dl>
 <dd>
 
@@ -5002,7 +5027,7 @@ await client.workflows.update("id", {
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">delete</a>(id) -> phenoml.WorkflowsDeleteResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">delete</a>(id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>