@ottolab/extraction 0.1.0

package/__tests__/llm-extractor.test.ts

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+import { describe, it, expect } from 'vitest';
+import { extractFromCsv } from '../src/llm-extractor.js';
+
+describe('extractFromCsv', () => {
+  it('should parse simple CSV with standard headers', () => {
+    const csv = `Total Cholesterol,LDL,HDL,Triglycerides,HbA1c
+200,120,55,130,5.4`;
+
+    const result = extractFromCsv(csv);
+    expect(result.total_cholesterol).toBe(200);
+    expect(result.ldl_c).toBe(120);
+    expect(result.hdl).toBe(55);
+    expect(result.triglycerides).toBe(130);
+    expect(result.hba1c).toBe(5.4);
+  });
+
+  it('should normalize common header aliases', () => {
+    const csv = `LDL-C,HDL-C,A1C,Glucose,SGPT
+110,58,5.2,92,25`;
+
+    const result = extractFromCsv(csv);
+    expect(result.ldl_c).toBe(110);
+    expect(result.hdl).toBe(58);
+    expect(result.hba1c).toBe(5.2);
+    expect(result.fasting_glucose).toBe(92);
+    expect(result.alt).toBe(25);
+  });
+
+  it('should handle empty values', () => {
+    const csv = `Total Cholesterol,LDL,HDL
+200,,55`;
+
+    const result = extractFromCsv(csv);
+    expect(result.total_cholesterol).toBe(200);
+    expect(result.hdl).toBe(55);
+    expect(result.ldl_c).toBeUndefined();
+  });
+
+  it('should throw on single-line CSV (no data row)', () => {
+    expect(() => extractFromCsv('Total Cholesterol,LDL,HDL')).toThrow(
+      'at least a header row and a data row',
+    );
+  });
+
+  it('should handle case-insensitive headers', () => {
+    const csv = `CREATININE,BUN,eGFR
+0.9,15,95`;
+
+    const result = extractFromCsv(csv);
+    expect(result.creatinine).toBe(0.9);
+    expect(result.bun).toBe(15);
+    expect(result.egfr).toBe(95);
+  });
+
+  it('should preserve non-numeric values as strings', () => {
+    const csv = `Albumin,Notes
+4.2,Normal`;
+
+    const result = extractFromCsv(csv);
+    expect(result.albumin).toBe(4.2);
+    expect(result.notes).toBe('Normal');
+  });
+
+  it('should handle whitespace in headers and values', () => {
+    const csv = ` Total Cholesterol , LDL , HDL
+ 200 , 120 , 55 `;
+
+    const result = extractFromCsv(csv);
+    expect(result.total_cholesterol).toBe(200);
+    expect(result.ldl_c).toBe(120);
+    expect(result.hdl).toBe(55);
+  });
+});

package/__tests__/validator.test.ts

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+import { describe, it, expect } from 'vitest';
+import { validateExtraction, CLINICAL_RANGES, BIOMARKER_MAP } from '../src/validator.js';
+import type { RawBiomarkers } from '../src/llm-extractor.js';
+
+describe('CLINICAL_RANGES', () => {
+  it('should have ranges for all mapped biomarkers', () => {
+    for (const key of Object.keys(BIOMARKER_MAP)) {
+      expect(CLINICAL_RANGES[key]).toBeDefined();
+    }
+  });
+
+  it('should have low < high for all ranges', () => {
+    for (const [key, [low, high]] of Object.entries(CLINICAL_RANGES)) {
+      expect(low).toBeLessThan(high);
+      expect(low).toBeTypeOf('number');
+      expect(high).toBeTypeOf('number');
+      // Verify key exists
+      expect(key).toBeTruthy();
+    }
+  });
+});
+
+describe('validateExtraction', () => {
+  it('should accept valid biomarkers within range', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: 200,
+      ldl_c: 120,
+      hdl: 55,
+      triglycerides: 130,
+      hba1c: 5.4,
+      fasting_glucose: 95,
+      creatinine: 0.9,
+      albumin: 4.2,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(8);
+    expect(result.rejected).toBe(0);
+    expect(result.biomarkers.totalCholesterol?.value).toBe(200);
+    expect(result.biomarkers.ldlC?.value).toBe(120);
+    expect(result.biomarkers.hdl?.value).toBe(55);
+    expect(result.biomarkers.albumin?.value).toBe(4.2);
+  });
+
+  it('should reject values outside clinical ranges', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: 9999, // way too high
+      hdl: -5, // negative
+      hba1c: 5.4, // valid
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(1); // only hba1c
+    expect(result.rejected).toBe(2);
+    expect(result.biomarkers.hba1c?.value).toBe(5.4);
+    expect(result.biomarkers.totalCholesterol).toBeUndefined();
+    expect(result.biomarkers.hdl).toBeUndefined();
+  });
+
+  it('should skip null and undefined values', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: null,
+      ldl_c: 100,
+      hdl: null,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(1);
+    expect(result.biomarkers.ldlC?.value).toBe(100);
+  });
+
+  it('should skip string values (qualitative results)', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: 200,
+      some_qualitative: 'Negative',
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(1);
+    expect(result.rejected).toBe(0);
+  });
+
+  it('should skip gender field', () => {
+    const raw: RawBiomarkers = {
+      gender: 'm',
+      total_cholesterol: 200,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(1);
+  });
+
+  it('should reject non-finite numbers', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: NaN,
+      ldl_c: Infinity,
+      hdl: 55,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(1);
+    expect(result.rejected).toBe(2);
+  });
+
+  it('should map to correct BiomarkerSet fields', () => {
+    const raw: RawBiomarkers = {
+      hs_crp: 1.5,
+      vitamin_d: 45,
+      lymphocyte_percent: 30,
+      bilirubin_total: 0.8,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.biomarkers.hsCrp?.value).toBe(1.5);
+    expect(result.biomarkers.hsCrp?.unit).toBe('mg/L');
+    expect(result.biomarkers.vitaminD?.value).toBe(45);
+    expect(result.biomarkers.lymphocytePercent?.value).toBe(30);
+    expect(result.biomarkers.bilirubinTotal?.value).toBe(0.8);
+  });
+
+  it('should include unit and name in BiomarkerValue', () => {
+    const raw: RawBiomarkers = { alt: 25 };
+    const result = validateExtraction(raw);
+    expect(result.biomarkers.alt).toEqual({
+      name: 'ALT',
+      value: 25,
+      unit: 'U/L',
+    });
+  });
+
+  it('should record rejections with reasons', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: 9999,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.rejections.length).toBe(1);
+    expect(result.rejections[0].key).toBe('total_cholesterol');
+    expect(result.rejections[0].reason).toContain('outside clinical range');
+  });
+
+  it('should compute reasonable confidence for good extraction', () => {
+    const raw: RawBiomarkers = {
+      total_cholesterol: 200,
+      ldl_c: 120,
+      hdl: 55,
+      triglycerides: 130,
+      hba1c: 5.4,
+      fasting_glucose: 95,
+      creatinine: 0.9,
+      albumin: 4.2,
+      alt: 25,
+      ast: 22,
+      wbc: 7.0,
+      hemoglobin: 14.5,
+      platelets: 250,
+      mcv: 90,
+      rdw: 13,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.confidence).toBeGreaterThan(0.7);
+  });
+
+  it('should return 0 confidence for empty extraction', () => {
+    const result = validateExtraction({});
+    expect(result.confidence).toBe(0);
+    expect(result.accepted).toBe(0);
+  });
+
+  it('should reduce confidence when HDL > total cholesterol', () => {
+    const consistent: RawBiomarkers = {
+      total_cholesterol: 200,
+      hdl: 55,
+      ldl_c: 120,
+      hba1c: 5.4,
+      creatinine: 0.9,
+    };
+    const inconsistent: RawBiomarkers = {
+      total_cholesterol: 100,
+      hdl: 150, // impossible: HDL > total
+      ldl_c: 120,
+      hba1c: 5.4,
+      creatinine: 0.9,
+    };
+
+    const c1 = validateExtraction(consistent).confidence;
+    // HDL=150 is within range [5,150] so it passes range check but fails consistency
+    // However total_cholesterol=100 makes HDL > total
+    const c2 = validateExtraction(inconsistent).confidence;
+    expect(c2).toBeLessThan(c1);
+  });
+
+  it('should handle all target biomarkers', () => {
+    const raw: RawBiomarkers = {
+      weight_kg: 75,
+      height_cm: 175,
+      bmi: 24.5,
+      body_fat_percent: 18,
+      systolic_bp: 120,
+      diastolic_bp: 75,
+      heart_rate: 68,
+      total_cholesterol: 195,
+      ldl_c: 110,
+      hdl: 58,
+      triglycerides: 120,
+      apoB: 85,
+      hba1c: 5.3,
+      fasting_glucose: 88,
+      fasting_insulin: 5.5,
+      uric_acid: 5.2,
+      creatinine: 0.95,
+      bun: 15,
+      egfr: 95,
+      alt: 22,
+      ast: 20,
+      alp: 70,
+      ggt: 25,
+      bilirubin_total: 0.7,
+      albumin: 4.3,
+      hs_crp: 0.8,
+      esr: 8,
+      cortisol: 12,
+      testosterone: 550,
+      estradiol: 25,
+      tsh: 1.8,
+      wbc: 6.5,
+      rbc: 4.8,
+      hemoglobin: 14.8,
+      hematocrit: 44,
+      platelets: 240,
+      mcv: 88,
+      rdw: 12.8,
+      lymphocyte_percent: 32,
+      vitamin_d: 48,
+    };
+
+    const result = validateExtraction(raw);
+    expect(result.accepted).toBe(40);
+    expect(result.rejected).toBe(0);
+    expect(result.confidence).toBeGreaterThan(0.8);
+  });
+});

package/package.json

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+{
+  "name": "@ottolab/extraction",
+  "version": "0.1.0",
+  "license": "MIT",
+  "repository": "https://github.com/hokev/Otto",
+  "publishConfig": { "access": "public" },
+  "type": "module",
+  "exports": {
+    ".": {
+      "import": {
+        "types": "./dist/index.d.ts",
+        "default": "./dist/index.js"
+      },
+      "source": "./src/index.ts"
+    }
+  },
+  "scripts": {
+    "build": "tsc --build",
+    "lint": "eslint src/",
+    "test": "vitest run"
+  },
+  "dependencies": {
+    "@ottolab/shared": "*"
+  },
+  "devDependencies": {
+    "vitest": "^3.0.0"
+  }
+}

package/src/index.ts

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+import type { ExtractionResult, ExtendedLLMProvider } from '@ottolab/shared';
+import { detectLab } from './lab-detector.js';
+import { extractFromPdf, extractFromCsv } from './llm-extractor.js';
+import { validateExtraction } from './validator.js';
+
+export interface ParseInput {
+  /** Base64-encoded PDF data */
+  pdf?: string;
+  /** Raw CSV text */
+  csv?: string;
+}
+
+/**
+ * Main extraction pipeline.
+ *
+ * PDF flow:
+ *   1. Lab Detection (LLM classify → Quest | LabCorp | international | unknown)
+ *   2. Structured Extraction (LLM multimodal + lab-specific few-shot)
+ *   3. Validation (clinical range checks, cross-biomarker consistency, confidence)
+ *
+ * CSV flow:
+ *   1. Column parsing + header normalization
+ *   2. Validation
+ */
+export async function runExtractionPipeline(
+  input: ParseInput,
+  provider?: ExtendedLLMProvider,
+): Promise<ExtractionResult> {
+  if (input.pdf) {
+    if (!provider) throw new Error('LLM provider required for PDF extraction');
+
+    // Step 1: Detect lab source
+    const detection = await detectLab(input.pdf, provider);
+
+    // Step 2: Extract biomarkers with lab-specific prompt
+    const raw = await extractFromPdf(input.pdf, detection.lab, provider);
+
+    // Step 3: Validate and transform
+    const validation = validateExtraction(raw);
+
+    return {
+      biomarkers: validation.biomarkers,
+      sourceLab: detection.lab,
+      sourceLanguage: detection.language,
+      confidence: validation.confidence,
+    };
+  }
+
+  if (input.csv) {
+    // CSV extraction (no LLM needed)
+    const raw = extractFromCsv(input.csv);
+    const validation = validateExtraction(raw);
+
+    return {
+      biomarkers: validation.biomarkers,
+      sourceLab: 'unknown',
+      sourceLanguage: 'en',
+      confidence: validation.confidence,
+    };
+  }
+
+  throw new Error('Either pdf (base64) or csv text must be provided');
+}
+
+export { detectLab } from './lab-detector.js';
+export { extractFromPdf, extractFromCsv } from './llm-extractor.js';
+export { validateExtraction } from './validator.js';
+export type { RawBiomarkers } from './llm-extractor.js';
+export type { ValidationResult } from './validator.js';

package/src/lab-detector.ts

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+import type { SourceLab, ExtendedLLMProvider } from '@ottolab/shared';
+import { LAB_DETECTION_PROMPT } from './prompts/base.js';
+
+export interface LabDetectionResult {
+  lab: SourceLab;
+  language: string;
+  confidence: number;
+}
+
+/**
+ * Detect the source laboratory from a PDF using LLM classification.
+ * Sends the first page(s) to the LLM to identify Quest, LabCorp, etc.
+ */
+export async function detectLab(
+  pdfBase64: string,
+  provider: ExtendedLLMProvider,
+): Promise<LabDetectionResult> {
+  try {
+    const response = await provider.chatMultimodal(
+      [
+        { type: 'document', data: pdfBase64, mimeType: 'application/pdf' },
+        { type: 'text', text: LAB_DETECTION_PROMPT },
+      ],
+      { temperature: 0, maxTokens: 256, responseFormat: 'json' },
+    );
+
+    const parsed = parseJsonResponse<LabDetectionResult>(response);
+
+    // Validate lab value
+    const validLabs: SourceLab[] = ['quest', 'labcorp', 'international', 'unknown'];
+    if (!validLabs.includes(parsed.lab)) {
+      parsed.lab = 'unknown';
+    }
+
+    return {
+      lab: parsed.lab,
+      language: parsed.language || 'en',
+      confidence: Math.min(Math.max(parsed.confidence || 0, 0), 1),
+    };
+  } catch {
+    return { lab: 'unknown', language: 'en', confidence: 0 };
+  }
+}
+
+function parseJsonResponse<T>(text: string): T {
+  // Strip markdown code fences if present
+  let cleaned = text.trim();
+  if (cleaned.startsWith('```')) {
+    cleaned = cleaned.replace(/^```(?:json)?\s*/, '').replace(/\s*```$/, '');
+  }
+
+  // Find JSON object boundaries
+  const start = cleaned.indexOf('{');
+  const end = cleaned.lastIndexOf('}');
+  if (start === -1 || end === -1) {
+    throw new Error('No JSON object found in response');
+  }
+
+  return JSON.parse(cleaned.slice(start, end + 1)) as T;
+}

package/src/llm-extractor.ts

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+import type { SourceLab, ExtendedLLMProvider } from '@ottolab/shared';
+import { BASE_EXTRACTION_PROMPT } from './prompts/base.js';
+import { QUEST_EXTRACTION_PROMPT } from './prompts/quest.js';
+import { LABCORP_EXTRACTION_PROMPT } from './prompts/labcorp.js';
+
+/** Raw extraction output — flat key/value from LLM. */
+export type RawBiomarkers = Record<string, number | string | null>;
+
+/**
+ * Select the appropriate extraction prompt based on detected lab.
+ */
+function getPromptForLab(lab: SourceLab): string {
+  switch (lab) {
+    case 'quest':
+      return QUEST_EXTRACTION_PROMPT;
+    case 'labcorp':
+      return LABCORP_EXTRACTION_PROMPT;
+    default:
+      return BASE_EXTRACTION_PROMPT;
+  }
+}
+
+/**
+ * Extract biomarkers from a PDF using multimodal LLM.
+ *
+ * Sends the full PDF as base64 inline data with a lab-specific prompt.
+ * Returns raw key/value pairs (not yet validated or normalized).
+ */
+export async function extractFromPdf(
+  pdfBase64: string,
+  lab: SourceLab,
+  provider: ExtendedLLMProvider,
+): Promise<RawBiomarkers> {
+  const prompt = getPromptForLab(lab);
+
+  const response = await provider.chatMultimodal(
+    [
+      { type: 'document', data: pdfBase64, mimeType: 'application/pdf' },
+      { type: 'text', text: prompt },
+    ],
+    { temperature: 0, maxTokens: 4096, responseFormat: 'json' },
+  );
+
+  return parseExtractionResponse(response);
+}
+
+/**
+ * Extract biomarkers from CSV text.
+ *
+ * Expects a simple CSV with header row containing biomarker names
+ * and a single data row with values.
+ */
+export function extractFromCsv(csvText: string): RawBiomarkers {
+  const lines = csvText.trim().split('\n');
+  if (lines.length < 2) {
+    throw new Error('CSV must have at least a header row and a data row');
+  }
+
+  const headers = lines[0].split(',').map((h) => h.trim().toLowerCase());
+  const values = lines[1].split(',').map((v) => v.trim());
+
+  const result: RawBiomarkers = {};
+  for (let i = 0; i < headers.length; i++) {
+    const key = normalizeHeaderName(headers[i]);
+    const raw = values[i];
+    if (!key || !raw || raw === '') continue;
+
+    const num = parseFloat(raw);
+    result[key] = Number.isNaN(num) ? raw : num;
+  }
+
+  return result;
+}
+
+/**
+ * Normalize CSV header names to our canonical biomarker keys.
+ */
+function normalizeHeaderName(header: string): string {
+  const mappings: Record<string, string> = {
+    'total cholesterol': 'total_cholesterol',
+    cholesterol: 'total_cholesterol',
+    'ldl-c': 'ldl_c',
+    ldl: 'ldl_c',
+    'hdl-c': 'hdl',
+    hdl: 'hdl',
+    triglycerides: 'triglycerides',
+    tg: 'triglycerides',
+    hba1c: 'hba1c',
+    a1c: 'hba1c',
+    glucose: 'fasting_glucose',
+    'fasting glucose': 'fasting_glucose',
+    insulin: 'fasting_insulin',
+    'fasting insulin': 'fasting_insulin',
+    'uric acid': 'uric_acid',
+    creatinine: 'creatinine',
+    bun: 'bun',
+    egfr: 'egfr',
+    alt: 'alt',
+    sgpt: 'alt',
+    ast: 'ast',
+    sgot: 'ast',
+    alp: 'alp',
+    ggt: 'ggt',
+    bilirubin: 'bilirubin_total',
+    albumin: 'albumin',
+    'hs-crp': 'hs_crp',
+    crp: 'hs_crp',
+    esr: 'esr',
+    cortisol: 'cortisol',
+    testosterone: 'testosterone',
+    estradiol: 'estradiol',
+    tsh: 'tsh',
+    wbc: 'wbc',
+    rbc: 'rbc',
+    hemoglobin: 'hemoglobin',
+    hgb: 'hemoglobin',
+    hematocrit: 'hematocrit',
+    hct: 'hematocrit',
+    platelets: 'platelets',
+    plt: 'platelets',
+    mcv: 'mcv',
+    rdw: 'rdw',
+    'lymphocyte %': 'lymphocyte_percent',
+    lymphocytes: 'lymphocyte_percent',
+    'vitamin d': 'vitamin_d',
+    '25-oh vitamin d': 'vitamin_d',
+    weight: 'weight_kg',
+    height: 'height_cm',
+    bmi: 'bmi',
+    'body fat': 'body_fat_percent',
+    'systolic bp': 'systolic_bp',
+    'diastolic bp': 'diastolic_bp',
+    'heart rate': 'heart_rate',
+    apob: 'apoB',
+    'apo b': 'apoB',
+  };
+
+  return mappings[header] ?? header.replace(/[\s-]+/g, '_').toLowerCase();
+}
+
+function parseExtractionResponse(text: string): RawBiomarkers {
+  let cleaned = text.trim();
+
+  // Strip markdown code fences
+  if (cleaned.startsWith('```')) {
+    cleaned = cleaned.replace(/^```(?:json)?\s*/, '').replace(/\s*```$/, '');
+  }
+
+  // Find JSON object
+  const start = cleaned.indexOf('{');
+  const end = cleaned.lastIndexOf('}');
+  if (start === -1 || end === -1) {
+    throw new Error('No JSON object found in LLM extraction response');
+  }
+
+  return JSON.parse(cleaned.slice(start, end + 1)) as RawBiomarkers;
+}

package/src/prompts/base.ts

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+/**
+ * Base extraction prompt — universal lab report parser.
+ *
+ * Used when lab source is unknown or for international labs.
+ * Instructs the LLM to extract structured biomarkers from any lab PDF.
+ */
+export const BASE_EXTRACTION_PROMPT = `You are a clinical laboratory data extraction system. Extract ALL biomarker values from this lab report into a structured JSON object.
+
+## Output Format
+
+Return ONLY a raw JSON object (no markdown, no explanation, no code fences). The JSON must have this exact structure:
+
+{
+  "gender": "m" or "f" or null,
+  "weight_kg": <number or null>,
+  "height_cm": <number or null>,
+  "bmi": <number or null>,
+  "body_fat_percent": <number or null>,
+  "systolic_bp": <number or null>,
+  "diastolic_bp": <number or null>,
+  "heart_rate": <number or null>,
+  "total_cholesterol": <mg/dL>,
+  "ldl_c": <mg/dL>,
+  "hdl": <mg/dL>,
+  "triglycerides": <mg/dL>,
+  "apoB": <mg/dL>,
+  "hba1c": <%>,
+  "fasting_glucose": <mg/dL>,
+  "fasting_insulin": <uIU/mL>,
+  "uric_acid": <mg/dL>,
+  "creatinine": <mg/dL>,
+  "bun": <mg/dL>,
+  "egfr": <mL/min/1.73m2>,
+  "alt": <U/L>,
+  "ast": <U/L>,
+  "alp": <U/L>,
+  "ggt": <U/L>,
+  "bilirubin_total": <mg/dL>,
+  "albumin": <g/dL>,
+  "hs_crp": <mg/L>,
+  "esr": <mm/hr>,
+  "cortisol": <ug/dL>,
+  "testosterone": <ng/dL>,
+  "estradiol": <pg/mL>,
+  "tsh": <mIU/L>,
+  "wbc": <10^3/uL>,
+  "rbc": <10^6/uL>,
+  "hemoglobin": <g/dL>,
+  "hematocrit": <%>,
+  "platelets": <10^3/uL>,
+  "mcv": <fL>,
+  "rdw": <%>,
+  "lymphocyte_percent": <%>,
+  "vitamin_d": <ng/mL>
+}
+
+## Critical Instructions
+
+1. Read EVERY page of the report. Parse ALL table rows, not just the first page.
+2. Use null for any value not found in the report.
+3. The report may be bilingual (e.g., Chinese/English, Spanish/English). Parse BOTH languages.
+4. For reference ranges, DO NOT include them in the output — only extract actual values.
+
+## Unit Conversions — apply these BEFORE outputting:
+
+- Cholesterol (Total, LDL, HDL): if mmol/L → multiply by 38.67 to get mg/dL
+- Triglycerides: if mmol/L → multiply by 88.57 to get mg/dL
+- Glucose: if mmol/L → multiply by 18.016 to get mg/dL
+- Creatinine: if µmol/L → divide by 88.4 to get mg/dL
+- Uric Acid: if µmol/L → divide by 59.48 to get mg/dL
+- Albumin: if g/L → divide by 10 to get g/dL
+- BUN: if mmol/L → multiply by 2.801 to get mg/dL
+- hs-CRP: if mg/dL → multiply by 10 to get mg/L
+- Bilirubin: if µmol/L → divide by 17.1 to get mg/dL
+- Hemoglobin: if g/L → divide by 10 to get g/dL
+- Vitamin D: if nmol/L → divide by 2.496 to get ng/mL
+
+Return ONLY the JSON object.`;
+
+/**
+ * Lab detection prompt — classify the source laboratory.
+ */
+export const LAB_DETECTION_PROMPT = `Analyze this lab report and classify its source. Return ONLY a JSON object:
+
+{
+  "lab": "quest" | "labcorp" | "international" | "unknown",
+  "language": "<ISO 639-1 code, e.g., en, zh, es>",
+  "confidence": <0.0 to 1.0>
+}
+
+Classification rules:
+- "quest": Quest Diagnostics reports — look for Quest logo, "Quest Diagnostics", QuestAssureD
+- "labcorp": LabCorp reports — look for LabCorp logo, "Laboratory Corporation of America"
+- "international": Non-US labs, reports in languages other than English, SI units throughout
+- "unknown": Cannot determine with confidence
+
+Return ONLY the JSON object.`;

package/src/prompts/labcorp.ts

@@ -0,0 +1,65 @@
+/**
+ * LabCorp-specific extraction prompt.
+ *
+ * LabCorp reports:
+ * - Dense tabular format, sometimes multi-column
+ * - Results in US conventional units
+ * - Flag column: H, L, *, or blank for normal
+ * - Often includes calculated values (LDL calc, eGFR, HOMA-IR)
+ * - NMR LipoProfile may have particle numbers (not standard lipid panel)
+ */
+export const LABCORP_EXTRACTION_PROMPT = `You are a clinical laboratory data extraction system specialized in LabCorp reports.
+
+## LabCorp Report Format Notes
+- Results are in US conventional units (mg/dL, g/dL, U/L) — use values as-is
+- Dense tabular layout, sometimes multi-column per page
+- Flags: H = high, L = low, * = critical
+- May include NMR LipoProfile — extract standard lipid values, not particle counts
+- eGFR and calculated LDL are often included as separate line items
+- CBC may show both relative (%) and absolute counts
+
+## Output Format
+
+Return ONLY a raw JSON object (no markdown, no code fences):
+
+{
+  "gender": "m" or "f" or null,
+  "weight_kg": <number or null>,
+  "height_cm": <number or null>,
+  "bmi": <number or null>,
+  "total_cholesterol": <mg/dL>,
+  "ldl_c": <mg/dL>,
+  "hdl": <mg/dL>,
+  "triglycerides": <mg/dL>,
+  "apoB": <mg/dL>,
+  "hba1c": <%>,
+  "fasting_glucose": <mg/dL>,
+  "fasting_insulin": <uIU/mL>,
+  "uric_acid": <mg/dL>,
+  "creatinine": <mg/dL>,
+  "bun": <mg/dL>,
+  "egfr": <mL/min/1.73m2>,
+  "alt": <U/L>,
+  "ast": <U/L>,
+  "alp": <U/L>,
+  "ggt": <U/L>,
+  "bilirubin_total": <mg/dL>,
+  "albumin": <g/dL>,
+  "hs_crp": <mg/L>,
+  "esr": <mm/hr>,
+  "cortisol": <ug/dL>,
+  "testosterone": <ng/dL>,
+  "estradiol": <pg/mL>,
+  "tsh": <mIU/L>,
+  "wbc": <10^3/uL>,
+  "rbc": <10^6/uL>,
+  "hemoglobin": <g/dL>,
+  "hematocrit": <%>,
+  "platelets": <10^3/uL>,
+  "mcv": <fL>,
+  "rdw": <%>,
+  "lymphocyte_percent": <%>,
+  "vitamin_d": <ng/mL>
+}
+
+Read EVERY page. Use null for values not found. Return ONLY the JSON.`;

package/src/prompts/quest.ts

@@ -0,0 +1,63 @@
+/**
+ * Quest Diagnostics-specific extraction prompt.
+ *
+ * Quest reports have a distinctive format:
+ * - Tabular layout with Test Name | Result | Flag | Reference Range
+ * - Results in US conventional units (mg/dL, g/dL, U/L)
+ * - Flags: H (high), L (low), * (critical)
+ * - Multi-page with patient demographics on page 1
+ */
+export const QUEST_EXTRACTION_PROMPT = `You are a clinical laboratory data extraction system specialized in Quest Diagnostics reports.
+
+## Quest Report Format Notes
+- Results are in US conventional units (mg/dL, g/dL, U/L) — use values as-is
+- Table columns: Test Name | Result | Flag | Reference Range
+- Flags: H = high, L = low, * = critical, A = abnormal
+- CBC differential may show both absolute counts and percentages
+- eGFR is often calculated and shown separately
+
+## Output Format
+
+Return ONLY a raw JSON object (no markdown, no code fences):
+
+{
+  "gender": "m" or "f" or null,
+  "weight_kg": <number or null>,
+  "height_cm": <number or null>,
+  "bmi": <number or null>,
+  "total_cholesterol": <mg/dL>,
+  "ldl_c": <mg/dL>,
+  "hdl": <mg/dL>,
+  "triglycerides": <mg/dL>,
+  "apoB": <mg/dL>,
+  "hba1c": <%>,
+  "fasting_glucose": <mg/dL>,
+  "fasting_insulin": <uIU/mL>,
+  "uric_acid": <mg/dL>,
+  "creatinine": <mg/dL>,
+  "bun": <mg/dL>,
+  "egfr": <mL/min/1.73m2>,
+  "alt": <U/L>,
+  "ast": <U/L>,
+  "alp": <U/L>,
+  "ggt": <U/L>,
+  "bilirubin_total": <mg/dL>,
+  "albumin": <g/dL>,
+  "hs_crp": <mg/L>,
+  "esr": <mm/hr>,
+  "cortisol": <ug/dL>,
+  "testosterone": <ng/dL>,
+  "estradiol": <pg/mL>,
+  "tsh": <mIU/L>,
+  "wbc": <10^3/uL>,
+  "rbc": <10^6/uL>,
+  "hemoglobin": <g/dL>,
+  "hematocrit": <%>,
+  "platelets": <10^3/uL>,
+  "mcv": <fL>,
+  "rdw": <%>,
+  "lymphocyte_percent": <%>,
+  "vitamin_d": <ng/mL>
+}
+
+Read EVERY page. Use null for values not found. Return ONLY the JSON.`;

package/src/validator.ts

@@ -0,0 +1,218 @@
+import type { BiomarkerValue, BiomarkerSet } from '@ottolab/shared';
+import type { RawBiomarkers } from './llm-extractor.js';
+
+/**
+ * Clinical ranges for validation — generous bounds to avoid false rejections.
+ * Values outside these ranges are likely extraction errors.
+ */
+const CLINICAL_RANGES: Record<string, [number, number]> = {
+  weight_kg: [20, 300],
+  height_cm: [100, 250],
+  bmi: [10, 60],
+  body_fat_percent: [2, 60],
+  systolic_bp: [60, 250],
+  diastolic_bp: [30, 150],
+  heart_rate: [30, 220],
+  total_cholesterol: [50, 500],
+  ldl_c: [10, 400],
+  hdl: [5, 150],
+  triglycerides: [10, 2000],
+  apoB: [10, 300],
+  hba1c: [3, 15],
+  fasting_glucose: [30, 500],
+  fasting_insulin: [0.5, 300],
+  uric_acid: [0.5, 20],
+  creatinine: [0.1, 15],
+  bun: [2, 100],
+  egfr: [5, 150],
+  alt: [1, 2000],
+  ast: [1, 2000],
+  alp: [10, 1000],
+  ggt: [1, 2000],
+  bilirubin_total: [0.05, 30],
+  albumin: [1, 6],
+  hs_crp: [0.01, 300],
+  esr: [0, 140],
+  cortisol: [0.5, 60],
+  testosterone: [1, 2000],
+  estradiol: [1, 5000],
+  tsh: [0.01, 100],
+  wbc: [1, 50],
+  rbc: [1, 10],
+  hemoglobin: [3, 25],
+  hematocrit: [15, 65],
+  platelets: [10, 1000],
+  mcv: [50, 130],
+  rdw: [9, 25],
+  lymphocyte_percent: [2, 70],
+  vitamin_d: [3, 200],
+};
+
+/**
+ * Map from raw extraction keys to BiomarkerSet field names and display metadata.
+ */
+const BIOMARKER_MAP: Record<string, { field: keyof BiomarkerSet; name: string; unit: string }> = {
+  weight_kg: { field: 'weight', name: 'Weight', unit: 'kg' },
+  height_cm: { field: 'height', name: 'Height', unit: 'cm' },
+  bmi: { field: 'bmi', name: 'BMI', unit: 'kg/m2' },
+  body_fat_percent: { field: 'bodyFatPercent', name: 'Body Fat', unit: '%' },
+  systolic_bp: { field: 'bloodPressureSystolic', name: 'Systolic BP', unit: 'mmHg' },
+  diastolic_bp: { field: 'bloodPressureDiastolic', name: 'Diastolic BP', unit: 'mmHg' },
+  heart_rate: { field: 'heartRate', name: 'Heart Rate', unit: 'bpm' },
+  total_cholesterol: { field: 'totalCholesterol', name: 'Total Cholesterol', unit: 'mg/dL' },
+  ldl_c: { field: 'ldlC', name: 'LDL-C', unit: 'mg/dL' },
+  hdl: { field: 'hdl', name: 'HDL', unit: 'mg/dL' },
+  triglycerides: { field: 'triglycerides', name: 'Triglycerides', unit: 'mg/dL' },
+  apoB: { field: 'apoB', name: 'ApoB', unit: 'mg/dL' },
+  hba1c: { field: 'hba1c', name: 'HbA1c', unit: '%' },
+  fasting_glucose: { field: 'fastingGlucose', name: 'Fasting Glucose', unit: 'mg/dL' },
+  fasting_insulin: { field: 'fastingInsulin', name: 'Fasting Insulin', unit: 'uIU/mL' },
+  uric_acid: { field: 'uricAcid', name: 'Uric Acid', unit: 'mg/dL' },
+  creatinine: { field: 'creatinine', name: 'Creatinine', unit: 'mg/dL' },
+  bun: { field: 'bun', name: 'BUN', unit: 'mg/dL' },
+  egfr: { field: 'egfr', name: 'eGFR', unit: 'mL/min/1.73m2' },
+  alt: { field: 'alt', name: 'ALT', unit: 'U/L' },
+  ast: { field: 'ast', name: 'AST', unit: 'U/L' },
+  alp: { field: 'alp', name: 'ALP', unit: 'U/L' },
+  ggt: { field: 'ggt', name: 'GGT', unit: 'U/L' },
+  bilirubin_total: { field: 'bilirubinTotal', name: 'Bilirubin (Total)', unit: 'mg/dL' },
+  albumin: { field: 'albumin', name: 'Albumin', unit: 'g/dL' },
+  hs_crp: { field: 'hsCrp', name: 'hs-CRP', unit: 'mg/L' },
+  esr: { field: 'esr', name: 'ESR', unit: 'mm/hr' },
+  cortisol: { field: 'cortisol', name: 'Cortisol', unit: 'ug/dL' },
+  testosterone: { field: 'testosterone', name: 'Testosterone', unit: 'ng/dL' },
+  estradiol: { field: 'estradiol', name: 'Estradiol', unit: 'pg/mL' },
+  tsh: { field: 'tsh', name: 'TSH', unit: 'mIU/L' },
+  wbc: { field: 'wbc', name: 'WBC', unit: '10^3/uL' },
+  rbc: { field: 'rbc', name: 'RBC', unit: '10^6/uL' },
+  hemoglobin: { field: 'hemoglobin', name: 'Hemoglobin', unit: 'g/dL' },
+  hematocrit: { field: 'hematocrit', name: 'Hematocrit', unit: '%' },
+  platelets: { field: 'platelets', name: 'Platelets', unit: '10^3/uL' },
+  mcv: { field: 'mcv', name: 'MCV', unit: 'fL' },
+  rdw: { field: 'rdw', name: 'RDW', unit: '%' },
+  lymphocyte_percent: { field: 'lymphocytePercent', name: 'Lymphocyte %', unit: '%' },
+  vitamin_d: { field: 'vitaminD', name: 'Vitamin D', unit: 'ng/mL' },
+};
+
+export interface ValidationResult {
+  biomarkers: BiomarkerSet;
+  accepted: number;
+  rejected: number;
+  confidence: number;
+  rejections: { key: string; value: unknown; reason: string }[];
+}
+
+/**
+ * Validate and transform raw LLM extraction output to typed BiomarkerSet.
+ *
+ * Steps:
+ * 1. Filter nulls/undefined
+ * 2. Type-check numeric values
+ * 3. Range-check against generous clinical bounds
+ * 4. Map to BiomarkerSet fields
+ * 5. Compute extraction confidence score
+ */
+export function validateExtraction(raw: RawBiomarkers): ValidationResult {
+  const biomarkers: BiomarkerSet = {};
+  const rejections: { key: string; value: unknown; reason: string }[] = [];
+  let accepted = 0;
+  let rejected = 0;
+
+  for (const [key, value] of Object.entries(raw)) {
+    // Skip gender and non-biomarker fields
+    if (key === 'gender') continue;
+
+    // Skip null/undefined
+    if (value === null || value === undefined) continue;
+
+    // Skip string values (qualitative results like "Negative")
+    if (typeof value === 'string') continue;
+
+    // Must be a number at this point
+    if (typeof value !== 'number' || !Number.isFinite(value)) {
+      rejections.push({ key, value, reason: 'not a finite number' });
+      rejected++;
+      continue;
+    }
+
+    // Check clinical ranges
+    const range = CLINICAL_RANGES[key];
+    if (range && (value < range[0] || value > range[1])) {
+      rejections.push({
+        key,
+        value,
+        reason: `outside clinical range [${range[0]}, ${range[1]}]`,
+      });
+      rejected++;
+      continue;
+    }
+
+    // Map to BiomarkerSet
+    const mapping = BIOMARKER_MAP[key];
+    if (!mapping) continue; // skip unknown keys
+
+    const biomarkerValue: BiomarkerValue = {
+      name: mapping.name,
+      value,
+      unit: mapping.unit,
+    };
+
+    (biomarkers as Record<string, BiomarkerValue>)[mapping.field] = biomarkerValue;
+    accepted++;
+  }
+
+  // Confidence based on yield ratio and cross-checks
+  const confidence = computeConfidence(biomarkers, accepted, rejected);
+
+  return { biomarkers, accepted, rejected, confidence, rejections };
+}
+
+/**
+ * Compute extraction confidence score (0-1).
+ *
+ * Factors:
+ * - Yield: how many biomarkers were successfully extracted
+ * - Rejection rate: high rejections lower confidence
+ * - Cross-biomarker consistency checks
+ */
+function computeConfidence(biomarkers: BiomarkerSet, accepted: number, rejected: number): number {
+  if (accepted === 0) return 0;
+
+  // Base confidence from yield (diminishing returns above 15 markers)
+  const yieldScore = Math.min(accepted / 15, 1.0);
+
+  // Penalty for rejections
+  const total = accepted + rejected;
+  const rejectionPenalty = total > 0 ? rejected / total : 0;
+
+  // Cross-biomarker consistency checks
+  let consistencyScore = 1.0;
+
+  // Check: if both ALT and AST exist, AST should generally be ≤ 2×ALT in healthy
+  if (biomarkers.alt && biomarkers.ast) {
+    if (biomarkers.ast.value > biomarkers.alt.value * 5) {
+      consistencyScore -= 0.1;
+    }
+  }
+
+  // Check: HDL should be less than total cholesterol
+  if (biomarkers.hdl && biomarkers.totalCholesterol) {
+    if (biomarkers.hdl.value > biomarkers.totalCholesterol.value) {
+      consistencyScore -= 0.15;
+    }
+  }
+
+  // Check: LDL should be less than total cholesterol
+  if (biomarkers.ldlC && biomarkers.totalCholesterol) {
+    if (biomarkers.ldlC.value > biomarkers.totalCholesterol.value) {
+      consistencyScore -= 0.15;
+    }
+  }
+
+  const raw =
+    yieldScore * 0.5 + (1 - rejectionPenalty) * 0.25 + Math.max(consistencyScore, 0) * 0.25;
+  return Math.round(Math.min(Math.max(raw, 0), 1) * 100) / 100;
+}
+
+// Export for testing
+export { CLINICAL_RANGES, BIOMARKER_MAP };

package/tsconfig.json

@@ -0,0 +1,10 @@
+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "composite": true,
+    "outDir": "dist",
+    "rootDir": "src"
+  },
+  "include": ["src"],
+  "references": [{ "path": "../shared" }]
+}

package/tsconfig.tsbuildinfo

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