phenoml 12.2.0 → 12.4.0

package/dist/cjs/BaseClient.js

@@ -43,8 +43,8 @@ function normalizeClientOptions(options) {
     const headers = (0, headers_js_1.mergeHeaders)({
         "X-Fern-Language": "JavaScript",
         "X-Fern-SDK-Name": "phenoml",
-        "X-Fern-SDK-Version": "12.2.0",
-        "User-Agent": "phenoml/12.2.0",
+        "X-Fern-SDK-Version": "12.4.0",
+        "User-Agent": "phenoml/12.4.0",
         "X-Fern-Runtime": core.RUNTIME.type,
         "X-Fern-Runtime-Version": core.RUNTIME.version,
     }, options === null || options === void 0 ? void 0 : options.headers);

package/dist/cjs/api/resources/construe/types/CodeCategory.d.ts

@@ -0,0 +1,9 @@
+/**
+ * A higher-level grouping (e.g. HPO category) for an extracted code.
+ */
+export interface CodeCategory {
+    /** Identifier for the category term (e.g. an HPO URI). */
+    uri: string;
+    /** Human-readable label for the category term. */
+    label: string;
+}

package/dist/cjs/api/resources/construe/types/CodeCategory.js

@@ -0,0 +1,3 @@
+"use strict";
+// This file was auto-generated by Fern from our API Definition.
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/cjs/api/resources/construe/types/ExtractRequestConfig.d.ts

@@ -1,5 +1,16 @@
 export interface ExtractRequestConfig {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     chunking_method?: ExtractRequestConfig.ChunkingMethod | undefined;
     /**
      * Maximum number of codes to extract per chunk. If not specified, uses system-specific defaults:
@@ -15,8 +26,14 @@ export interface ExtractRequestConfig {
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     validation_method?: ExtractRequestConfig.ValidationMethod | undefined;
+    /**
+     * Minimum Jaccard similarity (0.0-1.0) for a code to be considered valid
+     * when using the "chunk_code_jaccard_similarity" validation method. Ignored by other methods.
+     */
+    chunk_code_jaccard_similarity_filtering_threshold?: number | undefined;
     /** Whether to include explanations for why each code was extracted */
     include_rationale?: boolean | undefined;
     /** Whether to include ancestor/parent codes in the results */
@@ -26,9 +43,7 @@ export interface ExtractRequestConfig {
     /**
      * Whether to include source text citations for each extracted code.
      * Citations show the exact text spans (with character offsets) that led to each code.
-     * Only available when using chunking_method: "sentences".
-     * The "none" method returns full text as one chunk (not useful for citations).
-     * LLM-based chunking (paragraphs, topics, soap_note) does not support citations.
+     * Supported when chunking_method is "sentences", "clinical_ner_extract", or "fasthpocr".
      */
     include_citations?: boolean | undefined;
     /**
@@ -60,13 +75,26 @@ export interface ExtractRequestConfig {
     consistency_effort?: ExtractRequestConfig.ConsistencyEffort | undefined;
 }
 export declare namespace ExtractRequestConfig {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     const ChunkingMethod: {
         readonly None: "none";
         readonly Sentences: "sentences";
         readonly Paragraphs: "paragraphs";
         readonly Topics: "topics";
         readonly SoapNote: "soap_note";
+        readonly ClinicalNerExtract: "clinical_ner_extract";
+        readonly Fasthpocr: "fasthpocr";
     };
     type ChunkingMethod = (typeof ChunkingMethod)[keyof typeof ChunkingMethod];
     /**
@@ -74,11 +102,13 @@ export declare namespace ExtractRequestConfig {
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     const ValidationMethod: {
         readonly None: "none";
         readonly Simple: "simple";
         readonly MedicationSearch: "medication_search";
+        readonly ChunkCodeJaccardSimilarity: "chunk_code_jaccard_similarity";
     };
     type ValidationMethod = (typeof ValidationMethod)[keyof typeof ValidationMethod];
     /**

package/dist/cjs/api/resources/construe/types/ExtractRequestConfig.js

@@ -4,24 +4,39 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ExtractRequestConfig = void 0;
 var ExtractRequestConfig;
 (function (ExtractRequestConfig) {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     ExtractRequestConfig.ChunkingMethod = {
         None: "none",
         Sentences: "sentences",
         Paragraphs: "paragraphs",
         Topics: "topics",
         SoapNote: "soap_note",
+        ClinicalNerExtract: "clinical_ner_extract",
+        Fasthpocr: "fasthpocr",
     };
     /**
      * Method for validating extracted codes:
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     ExtractRequestConfig.ValidationMethod = {
         None: "none",
         Simple: "simple",
         MedicationSearch: "medication_search",
+        ChunkCodeJaccardSimilarity: "chunk_code_jaccard_similarity",
     };
     /**
      * How much effort to spend ensuring consistent results across repeated requests.

package/dist/cjs/api/resources/construe/types/ExtractedCodeResult.d.ts

@@ -19,4 +19,9 @@ export interface ExtractedCodeResult {
      * Ancestor codes do not receive citations.
      */
     citations?: phenoml.construe.Citation[] | undefined;
+    /**
+     * Higher-level groupings the extracted code belongs to (e.g. HPO category terms).
+     * Only populated by full-extraction chunking methods such as "fasthpocr".
+     */
+    categories?: phenoml.construe.CodeCategory[] | undefined;
 }

package/dist/cjs/api/resources/construe/types/index.d.ts

@@ -1,4 +1,5 @@
 export * from "./Citation.js";
+export * from "./CodeCategory.js";
 export * from "./CodeResponse.js";
 export * from "./CodeSystemDetails.js";
 export * from "./CodeSystemInfo.js";

package/dist/cjs/api/resources/construe/types/index.js

@@ -15,6 +15,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./Citation.js"), exports);
+__exportStar(require("./CodeCategory.js"), exports);
 __exportStar(require("./CodeResponse.js"), exports);
 __exportStar(require("./CodeSystemDetails.js"), exports);
 __exportStar(require("./CodeSystemInfo.js"), exports);

package/dist/cjs/api/resources/lang2Fhir/client/Client.d.ts

@@ -43,7 +43,7 @@ export declare class Lang2FhirClient {
      *
      * @example
      *     await client.lang2Fhir.createMulti({
-     *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+     *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
      *     })
      */
     createMulti(request: phenoml.lang2Fhir.CreateMultiRequest, requestOptions?: Lang2FhirClient.RequestOptions): core.HttpResponsePromise<phenoml.lang2Fhir.CreateMultiResponse>;

package/dist/cjs/api/resources/lang2Fhir/client/Client.js

@@ -130,7 +130,7 @@ class Lang2FhirClient {
      *
      * @example
      *     await client.lang2Fhir.createMulti({
-     *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+     *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
      *     })
      */
     createMulti(request, requestOptions) {

package/dist/cjs/api/resources/lang2Fhir/client/requests/CreateMultiRequest.d.ts

@@ -1,7 +1,7 @@
 /**
  * @example
  *     {
- *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+ *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
  *     }
  */
 export interface CreateMultiRequest {

package/dist/cjs/version.d.ts

@@ -1 +1 @@
-export declare const SDK_VERSION = "12.2.0";
+export declare const SDK_VERSION = "12.4.0";

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SDK_VERSION = void 0;
-exports.SDK_VERSION = "12.2.0";
+exports.SDK_VERSION = "12.4.0";

package/dist/esm/BaseClient.mjs

@@ -6,8 +6,8 @@ export function normalizeClientOptions(options) {
     const headers = mergeHeaders({
         "X-Fern-Language": "JavaScript",
         "X-Fern-SDK-Name": "phenoml",
-        "X-Fern-SDK-Version": "12.2.0",
-        "User-Agent": "phenoml/12.2.0",
+        "X-Fern-SDK-Version": "12.4.0",
+        "User-Agent": "phenoml/12.4.0",
         "X-Fern-Runtime": core.RUNTIME.type,
         "X-Fern-Runtime-Version": core.RUNTIME.version,
     }, options === null || options === void 0 ? void 0 : options.headers);

package/dist/esm/api/resources/construe/types/CodeCategory.d.mts

@@ -0,0 +1,9 @@
+/**
+ * A higher-level grouping (e.g. HPO category) for an extracted code.
+ */
+export interface CodeCategory {
+    /** Identifier for the category term (e.g. an HPO URI). */
+    uri: string;
+    /** Human-readable label for the category term. */
+    label: string;
+}

package/dist/esm/api/resources/construe/types/CodeCategory.mjs

@@ -0,0 +1,2 @@
+// This file was auto-generated by Fern from our API Definition.
+export {};

package/dist/esm/api/resources/construe/types/ExtractRequestConfig.d.mts

@@ -1,5 +1,16 @@
 export interface ExtractRequestConfig {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     chunking_method?: ExtractRequestConfig.ChunkingMethod | undefined;
     /**
      * Maximum number of codes to extract per chunk. If not specified, uses system-specific defaults:
@@ -15,8 +26,14 @@ export interface ExtractRequestConfig {
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     validation_method?: ExtractRequestConfig.ValidationMethod | undefined;
+    /**
+     * Minimum Jaccard similarity (0.0-1.0) for a code to be considered valid
+     * when using the "chunk_code_jaccard_similarity" validation method. Ignored by other methods.
+     */
+    chunk_code_jaccard_similarity_filtering_threshold?: number | undefined;
     /** Whether to include explanations for why each code was extracted */
     include_rationale?: boolean | undefined;
     /** Whether to include ancestor/parent codes in the results */
@@ -26,9 +43,7 @@ export interface ExtractRequestConfig {
     /**
      * Whether to include source text citations for each extracted code.
      * Citations show the exact text spans (with character offsets) that led to each code.
-     * Only available when using chunking_method: "sentences".
-     * The "none" method returns full text as one chunk (not useful for citations).
-     * LLM-based chunking (paragraphs, topics, soap_note) does not support citations.
+     * Supported when chunking_method is "sentences", "clinical_ner_extract", or "fasthpocr".
      */
     include_citations?: boolean | undefined;
     /**
@@ -60,13 +75,26 @@ export interface ExtractRequestConfig {
     consistency_effort?: ExtractRequestConfig.ConsistencyEffort | undefined;
 }
 export declare namespace ExtractRequestConfig {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     const ChunkingMethod: {
         readonly None: "none";
         readonly Sentences: "sentences";
         readonly Paragraphs: "paragraphs";
         readonly Topics: "topics";
         readonly SoapNote: "soap_note";
+        readonly ClinicalNerExtract: "clinical_ner_extract";
+        readonly Fasthpocr: "fasthpocr";
     };
     type ChunkingMethod = (typeof ChunkingMethod)[keyof typeof ChunkingMethod];
     /**
@@ -74,11 +102,13 @@ export declare namespace ExtractRequestConfig {
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     const ValidationMethod: {
         readonly None: "none";
         readonly Simple: "simple";
         readonly MedicationSearch: "medication_search";
+        readonly ChunkCodeJaccardSimilarity: "chunk_code_jaccard_similarity";
     };
     type ValidationMethod = (typeof ValidationMethod)[keyof typeof ValidationMethod];
     /**

package/dist/esm/api/resources/construe/types/ExtractRequestConfig.mjs

@@ -1,24 +1,39 @@
 // This file was auto-generated by Fern from our API Definition.
 export var ExtractRequestConfig;
 (function (ExtractRequestConfig) {
-    /** Method for splitting input text into chunks before code extraction */
+    /**
+     * Method for splitting input text into chunks before code extraction.
+     * * none - Treat the full input as a single chunk.
+     * * sentences - Split on sentence boundaries (supports citations).
+     * * paragraphs / topics / soap_note - LLM-based chunking.
+     * * clinical_ner_extract - Extract clinical concepts (problems, tests,
+     *   treatments) and use each as a chunk (supports citations).
+     * * fasthpocr - Extract HPO concepts directly with category
+     *   annotations (supports citations). Requires `system: HPO`;
+     *   other systems are rejected. Causes most other config options
+     *   to be ignored.
+     */
     ExtractRequestConfig.ChunkingMethod = {
         None: "none",
         Sentences: "sentences",
         Paragraphs: "paragraphs",
         Topics: "topics",
         SoapNote: "soap_note",
+        ClinicalNerExtract: "clinical_ner_extract",
+        Fasthpocr: "fasthpocr",
     };
     /**
      * Method for validating extracted codes:
      * * none - No validation, returns all candidate codes
      * * simple - LLM-based validation
      * * medication_search - LLM-based validation tailored for medication concepts
+     * * chunk_code_jaccard_similarity - Token-level Jaccard similarity between source text chunk and code description
      */
     ExtractRequestConfig.ValidationMethod = {
         None: "none",
         Simple: "simple",
         MedicationSearch: "medication_search",
+        ChunkCodeJaccardSimilarity: "chunk_code_jaccard_similarity",
     };
     /**
      * How much effort to spend ensuring consistent results across repeated requests.

package/dist/esm/api/resources/construe/types/ExtractedCodeResult.d.mts

@@ -19,4 +19,9 @@ export interface ExtractedCodeResult {
      * Ancestor codes do not receive citations.
      */
     citations?: phenoml.construe.Citation[] | undefined;
+    /**
+     * Higher-level groupings the extracted code belongs to (e.g. HPO category terms).
+     * Only populated by full-extraction chunking methods such as "fasthpocr".
+     */
+    categories?: phenoml.construe.CodeCategory[] | undefined;
 }

package/dist/esm/api/resources/construe/types/index.d.mts

@@ -1,4 +1,5 @@
 export * from "./Citation.mjs";
+export * from "./CodeCategory.mjs";
 export * from "./CodeResponse.mjs";
 export * from "./CodeSystemDetails.mjs";
 export * from "./CodeSystemInfo.mjs";

package/dist/esm/api/resources/construe/types/index.mjs

@@ -1,4 +1,5 @@
 export * from "./Citation.mjs";
+export * from "./CodeCategory.mjs";
 export * from "./CodeResponse.mjs";
 export * from "./CodeSystemDetails.mjs";
 export * from "./CodeSystemInfo.mjs";

package/dist/esm/api/resources/lang2Fhir/client/Client.d.mts

@@ -43,7 +43,7 @@ export declare class Lang2FhirClient {
      *
      * @example
      *     await client.lang2Fhir.createMulti({
-     *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+     *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
      *     })
      */
     createMulti(request: phenoml.lang2Fhir.CreateMultiRequest, requestOptions?: Lang2FhirClient.RequestOptions): core.HttpResponsePromise<phenoml.lang2Fhir.CreateMultiResponse>;

package/dist/esm/api/resources/lang2Fhir/client/Client.mjs

@@ -94,7 +94,7 @@ export class Lang2FhirClient {
      *
      * @example
      *     await client.lang2Fhir.createMulti({
-     *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+     *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
      *     })
      */
     createMulti(request, requestOptions) {

package/dist/esm/api/resources/lang2Fhir/client/requests/CreateMultiRequest.d.mts

@@ -1,7 +1,7 @@
 /**
  * @example
  *     {
- *         text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+ *         text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
  *     }
  */
 export interface CreateMultiRequest {

package/dist/esm/version.d.mts

@@ -1 +1 @@
-export declare const SDK_VERSION = "12.2.0";
+export declare const SDK_VERSION = "12.4.0";

package/dist/esm/version.mjs

@@ -1 +1 @@
-export const SDK_VERSION = "12.2.0";
+export const SDK_VERSION = "12.4.0";

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "phenoml",
-    "version": "12.2.0",
+    "version": "12.4.0",
     "private": false,
     "repository": {
         "type": "git",

package/reference.md

@@ -3256,7 +3256,7 @@ Resources are linked with proper references (e.g., Conditions reference the Pati
 
 ```typescript
 await client.lang2Fhir.createMulti({
-    text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
+    text: "John Smith, male born on 1980-03-12, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily."
 });
 
 ```