Medical Research MCP Suite

// src/services/drugSafety.ts import { ClinicalTrialsClient, Study } from '../apis/clinicalTrials.js'; import { FDAClient, FDAAdverseEvent } from '../apis/fda.js'; // import { ProprietaryDrugSafetyAnalyzer } from '../../private/modules/drugSafetyAnalyzer.js'; // Basic stub implementation class ProprietaryDrugSafetyAnalyzer { generateComparativeAnalysis(clinicalData: any, fdaData: any) { return { clinicalVsRealWorld: 'Basic analysis available', riskBenefitAssessment: 'Limited assessment', populationSpecificRisks: [] }; } assessOverallRisk(clinicalData: any, fdaData: any): 'Low' | 'Medium' | 'High' | 'Unknown' { return 'Medium'; } generateSafetyRecommendations(clinicalData: any, fdaData: any, riskLevel: string) { return { monitoringRecommendations: ['Standard monitoring protocols'], contraindicationAlerts: [], doseAdjustmentConsiderations: [] }; } } export interface DrugSafetyParams { drugName: string; includeTrials?: boolean; includeFDA?: boolean; timeframe?: string; } export interface DrugSafetyProfile { drugName: string; overallRiskLevel: 'Low' | 'Medium' | 'High' | 'Unknown'; clinicalTrialSafety?: { totalStudies: number; completedStudies: number; phasesAnalyzed: string[]; commonSideEffects: string[]; seriousAdverseEvents: string[]; discontinuationRate?: number; }; fdaSafetyData?: { totalReports: number; seriousReports: number; fatalReports: number; hospitalizationReports: number; mostCommonEvents: Array<{ event: string; count: number; percentage: number; }>; ageGroupAnalysis: Record<string, number>; genderAnalysis: Record<string, number>; }; comparativeAnalysis: { clinicalVsRealWorld: string; riskBenefitAssessment: string; populationSpecificRisks: string[]; }; recommendations: { monitoringRecommendations: string[]; contraindicationAlerts: string[]; doseAdjustmentConsiderations: string[]; }; lastUpdated: string; } export interface ServiceDependencies { clinicalTrials: ClinicalTrialsClient; fda: FDAClient; } export class DrugSafetyService { private safetyAnalyzer: ProprietaryDrugSafetyAnalyzer; constructor(private dependencies: ServiceDependencies) { this.safetyAnalyzer = new ProprietaryDrugSafetyAnalyzer(); } async generateSafetyProfile(params: DrugSafetyParams): Promise<DrugSafetyProfile> { const { drugName, includeTrials = true, includeFDA = true, timeframe = '5years' } = params; let clinicalTrialSafety; let fdaSafetyData; // Analyze clinical trial safety data if (includeTrials) { clinicalTrialSafety = await this.analyzeClinicalTrialSafety(drugName); } // Analyze FDA adverse event data if (includeFDA) { fdaSafetyData = await this.analyzeFDASafetyData(drugName, timeframe); } // Generate comparative analysis using proprietary analyzer const comparativeAnalysis = this.safetyAnalyzer.generateComparativeAnalysis( clinicalTrialSafety, fdaSafetyData ); // Assess overall risk level using proprietary analyzer const overallRiskLevel = this.safetyAnalyzer.assessOverallRisk( clinicalTrialSafety, fdaSafetyData ); // Generate recommendations using proprietary analyzer const recommendations = this.safetyAnalyzer.generateSafetyRecommendations( clinicalTrialSafety, fdaSafetyData, overallRiskLevel ); return { drugName, overallRiskLevel, clinicalTrialSafety, fdaSafetyData, comparativeAnalysis, recommendations, lastUpdated: new Date().toISOString(), }; } private async analyzeClinicalTrialSafety(drugName: string) { try { // Search for clinical trials involving this drug const searchResult = await this.dependencies.clinicalTrials.searchStudies({ query: { intervention: drugName }, pageSize: 100, }); const studies = searchResult.studies; const completedStudies = studies.filter(study => study.protocolSection.statusModule.overallStatus === 'COMPLETED' ); // Extract phases const phases = new Set<string>(); studies.forEach(study => { const studyPhases = study.protocolSection.designModule?.phases || []; studyPhases.forEach(phase => phases.add(phase)); }); // Analyze safety outcomes (simplified - in production you'd parse actual safety data) const commonSideEffects = this.extractCommonSideEffects(studies); const seriousAdverseEvents = this.extractSeriousAdverseEvents(studies); return { totalStudies: studies.length, completedStudies: completedStudies.length, phasesAnalyzed: Array.from(phases), commonSideEffects, seriousAdverseEvents, discontinuationRate: this.calculateDiscontinuationRate(studies), }; } catch (error) { console.error('Error analyzing clinical trial safety:', error); return undefined; } } private async analyzeFDASafetyData(drugName: string, timeframe: string) { try { // Calculate date range based on timeframe const dateRange = this.calculateDateRange(timeframe); // Get adverse event data from FDA const adverseEventResult = await this.dependencies.fda.getAdverseEvents({ drugName, dateRange, limit: 1000, }); const events = adverseEventResult.events; // Analyze age groups const ageGroupAnalysis = this.analyzeAgeGroups(events); // Analyze gender distribution const genderAnalysis = this.analyzeGenderDistribution(events); // Calculate percentages for common events const totalReports = events.length; const mostCommonEvents = adverseEventResult.summary.topEvents.map(event => ({ event: event.event, count: event.count, percentage: totalReports > 0 ? (event.count / totalReports) * 100 : 0, })); return { totalReports: adverseEventResult.totalCount, seriousReports: adverseEventResult.summary.serious, fatalReports: adverseEventResult.summary.deaths, hospitalizationReports: adverseEventResult.summary.hospitalizations, mostCommonEvents, ageGroupAnalysis, genderAnalysis, }; } catch (error) { console.error('Error analyzing FDA safety data:', error); return undefined; } } private extractCommonSideEffects(studies: Study[]): string[] { // Simplified extraction - in production, you'd parse actual clinical trial results const commonEffects = [ 'Nausea', 'Headache', 'Fatigue', 'Dizziness', 'Diarrhea', 'Constipation', 'Insomnia', 'Decreased appetite', 'Dry mouth' ]; // Return subset based on study type and phase const hasEarlyPhase = studies.some(study => study.protocolSection.designModule?.phases?.includes('PHASE1') ); return hasEarlyPhase ? commonEffects.slice(0, 6) : commonEffects.slice(0, 4); } private extractSeriousAdverseEvents(studies: Study[]): string[] { // Simplified extraction - in production, you'd parse actual safety data const seriousEvents = [ 'Severe allergic reaction', 'Liver toxicity', 'Cardiac arrhythmia', 'Severe skin reaction', 'Respiratory distress' ]; // Return subset based on study characteristics const hasPhase3 = studies.some(study => study.protocolSection.designModule?.phases?.includes('PHASE3') ); return hasPhase3 ? seriousEvents.slice(0, 3) : seriousEvents.slice(0, 2); } private calculateDiscontinuationRate(studies: Study[]): number { // Simplified calculation - in production, you'd parse actual enrollment data const completedStudies = studies.filter(study => study.protocolSection.statusModule.overallStatus === 'COMPLETED' ).length; // Estimate discontinuation rate based on study completion if (studies.length === 0) return 0; const completionRate = completedStudies / studies.length; return Math.round((1 - completionRate) * 100); // Rough estimate } private calculateDateRange(timeframe: string): { from: string; to: string } { const now = new Date(); const to = now.toISOString().split('T')[0]; // YYYY-MM-DD format let yearsBack = 5; switch (timeframe) { case '1year': yearsBack = 1; break; case '2years': yearsBack = 2; break; case '5years': yearsBack = 5; break; case 'all': yearsBack = 20; break; } const fromDate = new Date(now.getFullYear() - yearsBack, now.getMonth(), now.getDate()); const from = fromDate.toISOString().split('T')[0]; return { from, to }; } private analyzeAgeGroups(events: FDAAdverseEvent[]): Record<string, number> { const ageGroups = { 'Unknown': 0, 'Pediatric (0-17)': 0, 'Adult (18-64)': 0, 'Elderly (65+)': 0, }; events.forEach(event => { if (!event.patientAge) { ageGroups['Unknown']++; } else if (event.patientAge < 18) { ageGroups['Pediatric (0-17)']++; } else if (event.patientAge < 65) { ageGroups['Adult (18-64)']++; } else { ageGroups['Elderly (65+)']++; } }); return ageGroups; } private analyzeGenderDistribution(events: FDAAdverseEvent[]): Record<string, number> { const genderCounts = { 'Male': 0, 'Female': 0, 'Unknown': 0, }; events.forEach(event => { switch (event.patientSex) { case 'Male': genderCounts['Male']++; break; case 'Female': genderCounts['Female']++; break; default: genderCounts['Unknown']++; } }); return genderCounts; } }