from tools.base import Tool from tools.utils import ToolExecutionError, logger from typing import Any, Dict, List, Union import re import json class SuggestJournalsForSubmissionTool(Tool): def openai_spec(self, legacy=False): return { "name": self.name, "description": self.description, "parameters": self.args_schema } """ Tool to suggest suitable academic journals for manuscript submission based on research content. This tool analyzes the title, abstract, and summary of research work and uses internet search to find journals that publish similar content. It returns journal recommendations with impact factors, publishers, and topic focus areas. """ def __init__(self) -> None: """ Initialize the SuggestJournalsForSubmissionTool with its name, description, and argument schema. """ super().__init__() self.name = "suggest_journals_for_submission" self.description = ( "Suggest suitable academic journals for manuscript submission based on research content. " "Analyzes title, abstract, and research summary to find journals that publish similar work. " "Returns journal recommendations with impact factors, publishers, and topic focus areas." ) self.args_schema = { "type": "object", "properties": { "title": { "type": "string", "description": "Title of the research paper or manuscript" }, "abstract": { "type": "string", "description": "Abstract or summary of the research work" }, "research_area": { "type": "string", "description": "Primary research area or field (e.g., infectious diseases, microbiology, epidemiology)" }, "study_type": { "type": "string", "description": "Type of study (e.g., clinical trial, case study, systematic review, laboratory research)" }, "target_audience": { "type": "string", "description": "Target audience (e.g., clinicians, researchers, public health professionals)", "default": "researchers" } }, "required": ["title", "abstract", "research_area"] } async def run( self, title: str, abstract: str, research_area: str, study_type: str = "", target_audience: str = "researchers" ) -> str: """ Suggest suitable journals for manuscript submission based on research content. Args: title (str): Title of the research paper abstract (str): Abstract or summary of the research research_area (str): Primary research area or field study_type (str): Type of study target_audience (str): Target audience for the research Returns: str: Formatted list of journal recommendations with details """ try: # Extract key terms and concepts from the research content search_terms = self._extract_key_terms(title, abstract, research_area, study_type) # Search for relevant journals using internet search journal_suggestions = await self._search_for_journals(search_terms, research_area) # Format the results for user display return self._format_journal_recommendations(journal_suggestions, title, research_area) except Exception as e: logger.error(f"SuggestJournalsForSubmissionTool failed: {e}", exc_info=True) raise ToolExecutionError(f"SuggestJournalsForSubmissionTool failed: {e}") def _extract_key_terms(self, title: str, abstract: str, research_area: str, study_type: str) -> List[str]: """ Extract key terms and concepts from the research content for journal searching. """ # Combine all text for analysis combined_text = f"{title} {abstract} {research_area} {study_type}".lower() # Comprehensive medical/research terms to prioritize across all ID-related fields medical_terms = [ # Core ID terms "antimicrobial", "antibiotic", "infection", "pathogen", "bacteria", "virus", "fungal", "parasitic", "resistance", "stewardship", "clinical", "epidemiology", "microbiology", "infectious disease", "outbreak", "surveillance", "treatment", "diagnosis", "therapy", "prevention", "control", # Healthcare settings "hospital", "healthcare", "patient", "medical", "pharmaceutical", "nosocomial", "community-acquired", "healthcare-associated", "ICU", "emergency", "outpatient", "inpatient", # Specific pathogens "MRSA", "VRE", "ESBL", "CRE", "C. difficile", "candidemia", "aspergillus", "tuberculosis", "HIV", "hepatitis", "influenza", "COVID", "SARS", "MERS", "zika", "dengue", "malaria", # Public health "public health", "global health", "health policy", "implementation", "quality improvement", "health systems", "health economics", "cost-effectiveness", "surveillance", "contact tracing", # Vaccines "vaccine", "vaccination", "immunization", "immunology", "immune response", "antibody", "immunocompromised", "herd immunity", "vaccine hesitancy", "vaccine safety", # Laboratory/Diagnostics "diagnostic", "laboratory", "PCR", "culture", "sensitivity", "susceptibility", "biomarker", "rapid test", "point-of-care", "molecular", "genomic", "sequencing", "proteomics", # Wound care "wound", "wound healing", "tissue repair", "surgical site infection", "chronic wound", "diabetic foot", "pressure ulcer", "biofilm", "debridement", "dressing", # Travel medicine "travel medicine", "tropical disease", "neglected tropical disease", "vector-borne", "malaria", "yellow fever", "typhoid", "traveler's diarrhea", "pre-travel", # Pediatric "pediatric", "children", "infant", "neonatal", "adolescent", "childhood vaccination", "pediatric HIV", "congenital infection", # HIV/STI "HIV", "AIDS", "antiretroviral", "PrEP", "sexually transmitted", "STI", "STD", "syphilis", "gonorrhea", "chlamydia", "herpes", "HPV", # One Health "one health", "zoonotic", "zoonosis", "veterinary", "animal health", "environmental health", "food safety", "antimicrobial use in animals", "wildlife disease", # Implementation/Policy "guideline", "protocol", "best practice", "evidence-based", "clinical decision support", "quality improvement", "patient safety", "health technology assessment" ] # Extract relevant medical terms present in the text found_terms = [term for term in medical_terms if term in combined_text] # Add research area and study type as key terms search_terms = [research_area] if study_type: search_terms.append(study_type) # Add found medical terms search_terms.extend(found_terms[:5]) # Limit to top 5 to avoid overly long queries return search_terms async def _search_for_journals(self, search_terms: List[str], research_area: str) -> List[Dict[str, Any]]: """ Search the internet for journals that publish work in the specified areas. """ from tools.internet_search import InternetSearchTool search_tool = InternetSearchTool() journals_found = [] # Search queries for different aspects search_queries = [ f"{research_area} journals impact factor publisher", f"academic journals {' '.join(search_terms[:3])} submission", f"best journals publish {research_area} research", f"infectious disease journals {' '.join(search_terms[:2])} scope" ] for query in search_queries: try: search_result = await search_tool.run(query, max_results=5) if isinstance(search_result, str): # Parse the search results to extract journal information parsed_journals = self._parse_journal_info_from_search(search_result, search_terms) journals_found.extend(parsed_journals) except Exception as e: logger.warning(f"Search query failed: {query}, Error: {e}") continue # Remove duplicates and return top 5 unique_journals = self._deduplicate_journals(journals_found) return unique_journals[:5] def _parse_journal_info_from_search(self, search_text: str, search_terms: List[str]) -> List[Dict[str, Any]]: """ Parse journal information from search results. """ journals = [] # Comprehensive journal database covering ID, microbiology, stewardship, public health, and related fields known_journals = { # High-Impact General Medical Journals "Nature": {"publisher": "Nature Publishing Group", "estimated_if": "64.8"}, "Science": {"publisher": "American Association for the Advancement of Science", "estimated_if": "56.9"}, "The Lancet": {"publisher": "Elsevier", "estimated_if": "202.7"}, "New England Journal of Medicine": {"publisher": "Massachusetts Medical Society", "estimated_if": "176.1"}, "JAMA": {"publisher": "American Medical Association", "estimated_if": "157.3"}, "The Lancet Global Health": {"publisher": "Elsevier", "estimated_if": "34.1"}, "Nature Medicine": {"publisher": "Nature Publishing Group", "estimated_if": "87.2"}, # Core Infectious Diseases Journals "Clinical Infectious Diseases": {"publisher": "Oxford University Press", "estimated_if": "20.0"}, "Journal of Infectious Diseases": {"publisher": "Oxford University Press", "estimated_if": "7.9"}, "The Lancet Infectious Diseases": {"publisher": "Elsevier", "estimated_if": "71.4"}, "Emerging Infectious Diseases": {"publisher": "Centers for Disease Control and Prevention", "estimated_if": "16.1"}, "International Journal of Infectious Diseases": {"publisher": "Elsevier", "estimated_if": "4.2"}, "BMC Infectious Diseases": {"publisher": "BioMed Central", "estimated_if": "3.7"}, "Infectious Diseases": {"publisher": "Taylor & Francis", "estimated_if": "2.8"}, "Current Opinion in Infectious Diseases": {"publisher": "Wolters Kluwer", "estimated_if": "4.1"}, "Expert Review of Anti-infective Therapy": {"publisher": "Taylor & Francis", "estimated_if": "4.8"}, # Antimicrobial/Stewardship Journals "Antimicrobial Agents and Chemotherapy": {"publisher": "American Society for Microbiology", "estimated_if": "5.8"}, "Journal of Antimicrobial Chemotherapy": {"publisher": "Oxford University Press", "estimated_if": "6.9"}, "International Journal of Antimicrobial Agents": {"publisher": "Elsevier", "estimated_if": "6.3"}, "Antibiotics": {"publisher": "MDPI", "estimated_if": "5.4"}, "Journal of Global Antimicrobial Resistance": {"publisher": "Elsevier", "estimated_if": "4.1"}, "Antimicrobial Resistance & Infection Control": {"publisher": "BioMed Central", "estimated_if": "4.8"}, "JAC-Antimicrobial Resistance": {"publisher": "Oxford University Press", "estimated_if": "3.9"}, # Infection Prevention & Control "Infection Control and Hospital Epidemiology": {"publisher": "Cambridge University Press", "estimated_if": "4.2"}, "Journal of Hospital Infection": {"publisher": "Elsevier", "estimated_if": "4.9"}, "American Journal of Infection Control": {"publisher": "Elsevier", "estimated_if": "3.8"}, "Journal of Infection Prevention": {"publisher": "SAGE Publications", "estimated_if": "2.1"}, "Infection Prevention in Practice": {"publisher": "Elsevier", "estimated_if": "2.5"}, # Microbiology Journals "Nature Microbiology": {"publisher": "Nature Publishing Group", "estimated_if": "31.8"}, "mBio": {"publisher": "American Society for Microbiology", "estimated_if": "7.9"}, "Journal of Clinical Microbiology": {"publisher": "American Society for Microbiology", "estimated_if": "6.1"}, "Applied and Environmental Microbiology": {"publisher": "American Society for Microbiology", "estimated_if": "4.8"}, "Frontiers in Microbiology": {"publisher": "Frontiers Media", "estimated_if": "6.1"}, "Microorganisms": {"publisher": "MDPI", "estimated_if": "4.5"}, "Clinical Microbiology Reviews": {"publisher": "American Society for Microbiology", "estimated_if": "36.8"}, "Journal of Medical Microbiology": {"publisher": "Microbiology Society", "estimated_if": "2.9"}, "Diagnostic Microbiology and Infectious Disease": {"publisher": "Elsevier", "estimated_if": "3.0"}, "European Journal of Clinical Microbiology & Infectious Diseases": {"publisher": "Springer", "estimated_if": "4.1"}, "Medical Mycology": {"publisher": "Oxford University Press", "estimated_if": "3.0"}, "Journal of Fungi": {"publisher": "MDPI", "estimated_if": "5.4"}, # HIV/AIDS Journals "Journal of Acquired Immune Deficiency Syndromes": {"publisher": "Wolters Kluwer", "estimated_if": "3.2"}, "AIDS": {"publisher": "Wolters Kluwer", "estimated_if": "4.6"}, "The Lancet HIV": {"publisher": "Elsevier", "estimated_if": "15.8"}, "Journal of the International AIDS Society": {"publisher": "Wiley", "estimated_if": "5.0"}, "Current HIV/AIDS Reports": {"publisher": "Springer", "estimated_if": "4.5"}, "AIDS Research and Human Retroviruses": {"publisher": "Mary Ann Liebert", "estimated_if": "2.5"}, "HIV Medicine": {"publisher": "Wiley", "estimated_if": "3.1"}, "Journal of HIV/AIDS & Social Services": {"publisher": "Taylor & Francis", "estimated_if": "1.8"}, # Public Health & Epidemiology "The Lancet Public Health": {"publisher": "Elsevier", "estimated_if": "50.9"}, "American Journal of Public Health": {"publisher": "American Public Health Association", "estimated_if": "9.9"}, "American Journal of Epidemiology": {"publisher": "Oxford University Press", "estimated_if": "6.4"}, "Epidemiology": {"publisher": "Wolters Kluwer", "estimated_if": "4.9"}, "International Journal of Epidemiology": {"publisher": "Oxford University Press", "estimated_if": "9.7"}, "Epidemiology and Infection": {"publisher": "Cambridge University Press", "estimated_if": "3.0"}, "BMC Public Health": {"publisher": "BioMed Central", "estimated_if": "4.5"}, "Global Health Action": {"publisher": "Taylor & Francis", "estimated_if": "3.8"}, "PLOS Global Public Health": {"publisher": "Public Library of Science", "estimated_if": "4.2"}, "Journal of Public Health Policy": {"publisher": "Palgrave Macmillan", "estimated_if": "2.4"}, "Health Affairs": {"publisher": "Project HOPE", "estimated_if": "8.6"}, # Vaccine Journals "Vaccine": {"publisher": "Elsevier", "estimated_if": "4.3"}, "Human Vaccines & Immunotherapeutics": {"publisher": "Taylor & Francis", "estimated_if": "4.1"}, "Vaccines": {"publisher": "MDPI", "estimated_if": "4.9"}, "Expert Review of Vaccines": {"publisher": "Taylor & Francis", "estimated_if": "5.9"}, "Vaccine: X": {"publisher": "Elsevier", "estimated_if": "3.5"}, "NPJ Vaccines": {"publisher": "Nature Publishing Group", "estimated_if": "9.3"}, "Clinical and Vaccine Immunology": {"publisher": "American Society for Microbiology", "estimated_if": "3.8"}, # Travel Medicine & Tropical Diseases "Journal of Travel Medicine": {"publisher": "Oxford University Press", "estimated_if": "6.9"}, "Travel Medicine and Infectious Disease": {"publisher": "Elsevier", "estimated_if": "6.6"}, "Tropical Medicine & International Health": {"publisher": "Wiley", "estimated_if": "3.5"}, "The American Journal of Tropical Medicine and Hygiene": {"publisher": "American Society of Tropical Medicine and Hygiene", "estimated_if": "2.9"}, "Transactions of The Royal Society of Tropical Medicine and Hygiene": {"publisher": "Oxford University Press", "estimated_if": "2.1"}, "PLOS Neglected Tropical Diseases": {"publisher": "Public Library of Science", "estimated_if": "4.0"}, # Wound Care & Tissue Repair "Wound Repair and Regeneration": {"publisher": "Wiley", "estimated_if": "3.8"}, "Wounds": {"publisher": "HMP Global", "estimated_if": "1.9"}, "International Wound Journal": {"publisher": "Wiley", "estimated_if": "2.8"}, "Journal of Wound Care": {"publisher": "Mark Allen Healthcare", "estimated_if": "1.5"}, "Advances in Wound Care": {"publisher": "Mary Ann Liebert", "estimated_if": "4.2"}, "Wound Medicine": {"publisher": "Elsevier", "estimated_if": "2.1"}, "Journal of Tissue Viability": {"publisher": "Elsevier", "estimated_if": "2.5"}, # Pediatric Infectious Diseases "Pediatric Infectious Disease Journal": {"publisher": "Wolters Kluwer", "estimated_if": "3.2"}, "Journal of the Pediatric Infectious Diseases Society": {"publisher": "Oxford University Press", "estimated_if": "2.8"}, "Current Opinion in Pediatric Infectious Diseases": {"publisher": "Wolters Kluwer", "estimated_if": "2.5"}, # Sexually Transmitted Infections "Sexually Transmitted Infections": {"publisher": "BMJ Publishing Group", "estimated_if": "4.8"}, "Sexually Transmitted Diseases": {"publisher": "Wolters Kluwer", "estimated_if": "3.2"}, "International Journal of STD & AIDS": {"publisher": "SAGE Publications", "estimated_if": "1.8"}, # Laboratory Medicine & Diagnostics "Clinical Chemistry": {"publisher": "Oxford University Press", "estimated_if": "8.3"}, "Journal of Clinical Laboratory Analysis": {"publisher": "Wiley", "estimated_if": "2.9"}, "Clinical Microbiology and Infection": {"publisher": "Elsevier", "estimated_if": "6.4"}, "Point of Care": {"publisher": "Wolters Kluwer", "estimated_if": "2.1"}, "Clinica Chimica Acta": {"publisher": "Elsevier", "estimated_if": "3.8"}, # Veterinary & One Health "One Health": {"publisher": "Elsevier", "estimated_if": "7.5"}, "EcoHealth": {"publisher": "Springer", "estimated_if": "3.8"}, "Journal of Veterinary Internal Medicine": {"publisher": "Wiley", "estimated_if": "2.8"}, "Veterinary Microbiology": {"publisher": "Elsevier", "estimated_if": "3.2"}, "Preventive Veterinary Medicine": {"publisher": "Elsevier", "estimated_if": "2.9"}, # Open Access & Multidisciplinary "PLOS ONE": {"publisher": "Public Library of Science", "estimated_if": "3.7"}, "PLOS Medicine": {"publisher": "Public Library of Science", "estimated_if": "13.8"}, "PLOS Pathogens": {"publisher": "Public Library of Science", "estimated_if": "7.2"}, "Scientific Reports": {"publisher": "Nature Publishing Group", "estimated_if": "4.6"}, "Journal of Clinical Medicine": {"publisher": "MDPI", "estimated_if": "4.9"}, "International Journal of Environmental Research and Public Health": {"publisher": "MDPI", "estimated_if": "4.6"}, "Pathogens": {"publisher": "MDPI", "estimated_if": "3.7"}, # Regional & Specialized Journals "Journal of Infection and Chemotherapy": {"publisher": "Elsevier", "estimated_if": "4.1"}, "Asian Pacific Journal of Tropical Medicine": {"publisher": "Wolters Kluwer", "estimated_if": "2.5"}, "Brazilian Journal of Infectious Diseases": {"publisher": "Elsevier", "estimated_if": "2.8"}, "International Journal of Infectious Diseases and Therapy": {"publisher": "SciTechnol", "estimated_if": "1.9"}, "Infection and Drug Resistance": {"publisher": "Dove Medical Press", "estimated_if": "4.2"}, "Journal of Infection in Developing Countries": {"publisher": "Journal of Infection in Developing Countries", "estimated_if": "1.8"}, # Implementation Science & Health Policy "Implementation Science": {"publisher": "BioMed Central", "estimated_if": "5.4"}, "Health Policy and Planning": {"publisher": "Oxford University Press", "estimated_if": "3.9"}, "BMC Health Services Research": {"publisher": "BioMed Central", "estimated_if": "2.8"}, "Journal of Hospital Medicine": {"publisher": "Wiley", "estimated_if": "2.9"} } # Search for journal mentions in the text search_text_lower = search_text.lower() for journal_name, details in known_journals.items(): if journal_name.lower() in search_text_lower: # Calculate relevance score based on search terms relevance_score = self._calculate_relevance_score(search_text, journal_name, search_terms) journal_info = { "name": journal_name, "publisher": details["publisher"], "impact_factor": details["estimated_if"], "relevance_score": relevance_score, "topics": self._get_journal_topics(journal_name), "scope": self._get_journal_scope(journal_name) } journals.append(journal_info) return journals def _calculate_relevance_score(self, search_text: str, journal_name: str, search_terms: List[str]) -> float: """ Calculate relevance score based on how many search terms appear near the journal name. """ search_text_lower = search_text.lower() journal_name_lower = journal_name.lower() # Find the position of the journal name journal_pos = search_text_lower.find(journal_name_lower) if journal_pos == -1: return 0.0 # Count search terms within 200 characters of the journal name context_start = max(0, journal_pos - 100) context_end = min(len(search_text), journal_pos + len(journal_name) + 100) context = search_text_lower[context_start:context_end] term_matches = sum(1 for term in search_terms if term.lower() in context) return term_matches / len(search_terms) if search_terms else 0.0 def _get_journal_topics(self, journal_name: str) -> str: """ Get typical topic areas for known journals. """ topic_mapping = { # Core Infectious Diseases "Clinical Infectious Diseases": "Clinical infectious diseases, antimicrobial therapy, hospital epidemiology", "Journal of Infectious Diseases": "Basic and clinical infectious disease research, pathogenesis, immunology", "The Lancet Infectious Diseases": "High-impact infectious disease research, global health, epidemiology", "Emerging Infectious Diseases": "Emerging pathogens, outbreak investigations, surveillance, zoonoses", "International Journal of Infectious Diseases": "Clinical infectious diseases, tropical medicine, travel health", "BMC Infectious Diseases": "Open access infectious disease research, clinical studies", "Infectious Diseases": "Clinical infectious diseases, case reports, therapeutic advances", "Current Opinion in Infectious Diseases": "Expert reviews, current trends in infectious diseases", "Expert Review of Anti-infective Therapy": "Antimicrobial therapy, drug development, clinical applications", # Antimicrobial/Stewardship "Antimicrobial Agents and Chemotherapy": "Antimicrobial research, drug development, resistance mechanisms", "Journal of Antimicrobial Chemotherapy": "Antimicrobial therapy, resistance, pharmacokinetics", "International Journal of Antimicrobial Agents": "Antimicrobial therapy, resistance, pharmacology", "Antibiotics": "Antibiotic research, development, resistance, stewardship", "Journal of Global Antimicrobial Resistance": "Antimicrobial resistance surveillance, global health", "Antimicrobial Resistance & Infection Control": "AMR prevention, stewardship, infection control", "JAC-Antimicrobial Resistance": "Open access antimicrobial resistance research", # Infection Prevention & Control "Infection Control and Hospital Epidemiology": "Healthcare epidemiology, infection prevention, patient safety", "Journal of Hospital Infection": "Healthcare-associated infections, infection control, stewardship", "American Journal of Infection Control": "Infection prevention, control practices, healthcare safety", "Journal of Infection Prevention": "Evidence-based infection prevention strategies", "Infection Prevention in Practice": "Practical infection prevention, implementation science", # Microbiology "Nature Microbiology": "High-impact microbiology, molecular mechanisms, microbiome", "mBio": "Microbial pathogenesis, antimicrobial resistance, microbiome", "Journal of Clinical Microbiology": "Clinical microbiology, diagnostics, laboratory medicine", "Applied and Environmental Microbiology": "Environmental microbiology, biotechnology, ecology", "Frontiers in Microbiology": "Microbial research, infectious diseases, antimicrobial resistance", "Microorganisms": "Microbiology, infectious agents, host-pathogen interactions", "Clinical Microbiology Reviews": "Comprehensive reviews in clinical microbiology", "Journal of Medical Microbiology": "Medical microbiology, pathogenesis, diagnostics", "Diagnostic Microbiology and Infectious Disease": "Diagnostic methods, clinical microbiology", "European Journal of Clinical Microbiology & Infectious Diseases": "Clinical microbiology, infectious diseases, epidemiology", "Medical Mycology": "Fungal infections, mycology, antifungal therapy", "Journal of Fungi": "Fungal biology, pathogenic fungi, antifungal research", # HIV/AIDS "Journal of Acquired Immune Deficiency Syndromes": "HIV/AIDS research, treatment, prevention", "AIDS": "HIV/AIDS clinical research, epidemiology, social aspects", "The Lancet HIV": "High-impact HIV research, global health, prevention", "Journal of the International AIDS Society": "HIV research, prevention, treatment access", "Current HIV/AIDS Reports": "HIV/AIDS reviews, current developments", "AIDS Research and Human Retroviruses": "HIV research, retrovirology, pathogenesis", "HIV Medicine": "Clinical HIV medicine, treatment, care management", "Journal of HIV/AIDS & Social Services": "HIV social services, community health", # Public Health & Epidemiology "The Lancet Public Health": "High-impact public health research, global health policy", "American Journal of Public Health": "Public health research, policy, community health", "American Journal of Epidemiology": "Epidemiological methods, disease surveillance", "Epidemiology": "Epidemiological research, methodology, disease patterns", "International Journal of Epidemiology": "Global epidemiology, population health", "Epidemiology and Infection": "Infectious disease epidemiology, transmission dynamics", "BMC Public Health": "Open access public health research", "Global Health Action": "Global health initiatives, implementation research", "PLOS Global Public Health": "Open access global public health research", "Journal of Public Health Policy": "Health policy analysis, implementation", "Health Affairs": "Health policy, healthcare systems, economics", # Vaccines "Vaccine": "Vaccine development, immunization, vaccine safety", "Human Vaccines & Immunotherapeutics": "Vaccine research, immunotherapy, clinical trials", "Vaccines": "Open access vaccine research, development, policy", "Expert Review of Vaccines": "Vaccine reviews, expert opinions, development", "Vaccine: X": "Open access vaccine research, novel platforms", "NPJ Vaccines": "High-impact vaccine research, novel approaches", "Clinical and Vaccine Immunology": "Vaccine immunology, clinical studies", # Travel Medicine & Tropical Diseases "Journal of Travel Medicine": "Travel health, tropical diseases, prevention", "Travel Medicine and Infectious Disease": "Travel-related infections, prevention strategies", "Tropical Medicine & International Health": "Tropical diseases, global health, resource-limited settings", "The American Journal of Tropical Medicine and Hygiene": "Tropical medicine, parasitology, vector-borne diseases", "Transactions of The Royal Society of Tropical Medicine and Hygiene": "Tropical medicine, global health research", "PLOS Neglected Tropical Diseases": "Neglected tropical diseases, drug development", # Wound Care "Wound Repair and Regeneration": "Wound healing, tissue regeneration, therapeutic approaches", "Wounds": "Clinical wound care, management strategies, case studies", "International Wound Journal": "Wound care research, healing mechanisms, treatments", "Journal of Wound Care": "Evidence-based wound care, clinical practice", "Advances in Wound Care": "Innovative wound care technologies, research", "Wound Medicine": "Wound pathophysiology, therapeutic interventions", "Journal of Tissue Viability": "Tissue viability, wound prevention, care strategies", # Pediatric Infectious Diseases "Pediatric Infectious Disease Journal": "Pediatric infections, childhood diseases, vaccines", "Journal of the Pediatric Infectious Diseases Society": "Pediatric ID research, clinical care", "Current Opinion in Pediatric Infectious Diseases": "Pediatric ID reviews, expert opinions", # Sexually Transmitted Infections "Sexually Transmitted Infections": "STI research, prevention, public health", "Sexually Transmitted Diseases": "STD clinical research, epidemiology, treatment", "International Journal of STD & AIDS": "STI/HIV research, global perspectives", # Laboratory Medicine "Clinical Chemistry": "Clinical laboratory science, diagnostics, biomarkers", "Journal of Clinical Laboratory Analysis": "Laboratory medicine, diagnostic methods", "Clinical Microbiology and Infection": "Clinical microbiology, infectious diseases", "Point of Care": "Point-of-care testing, rapid diagnostics", "Clinica Chimica Acta": "Clinical chemistry, laboratory medicine", # One Health & Veterinary "One Health": "Interdisciplinary health research, zoonoses, environmental health", "EcoHealth": "Ecosystem health, zoonotic diseases, environmental factors", "Journal of Veterinary Internal Medicine": "Veterinary medicine, animal health", "Veterinary Microbiology": "Veterinary microbiology, animal pathogens", "Preventive Veterinary Medicine": "Disease prevention in animals, epidemiology", # General Medical "The Lancet": "High-impact clinical research, global health", "New England Journal of Medicine": "High-impact clinical studies, therapeutic advances", "JAMA": "Clinical research, public health, medical education", "Nature Medicine": "Translational medicine, biomedical research", "The Lancet Global Health": "Global health research, health equity", # Open Access "PLOS ONE": "Multidisciplinary research including infectious diseases and microbiology", "PLOS Medicine": "Open access clinical research, global health", "PLOS Pathogens": "Pathogen biology, host-pathogen interactions", "Scientific Reports": "Multidisciplinary scientific research", "Journal of Clinical Medicine": "Clinical research across medical specialties including ID", "International Journal of Environmental Research and Public Health": "Environmental health, public health research", "Pathogens": "Pathogen research, infectious disease mechanisms", # Regional Journals "Journal of Infection and Chemotherapy": "Infectious diseases, antimicrobial therapy (Asian focus)", "Asian Pacific Journal of Tropical Medicine": "Tropical medicine, infectious diseases (Asia-Pacific)", "Brazilian Journal of Infectious Diseases": "Infectious diseases (Latin American focus)", "Infection and Drug Resistance": "Antimicrobial resistance, drug development", "Journal of Infection in Developing Countries": "Infectious diseases in resource-limited settings", # Implementation Science "Implementation Science": "Implementation research, evidence-based practice", "Health Policy and Planning": "Health systems, policy implementation", "BMC Health Services Research": "Health services research, quality improvement", "Journal of Hospital Medicine": "Hospital medicine, quality improvement, patient safety" } return topic_mapping.get(journal_name, "General medical and scientific research") def _get_journal_scope(self, journal_name: str) -> str: """ Get the scope and focus of known journals. """ scope_mapping = { # Core ID Journals "Clinical Infectious Diseases": "Clinical research with immediate relevance to patient care", "Journal of Infectious Diseases": "Basic science and clinical research in infectious diseases", "The Lancet Infectious Diseases": "High-impact infectious disease research for global audience", "Emerging Infectious Diseases": "CDC journal focusing on emerging and re-emerging infections", "International Journal of Infectious Diseases": "Global infectious disease research with clinical focus", "BMC Infectious Diseases": "Open access platform for infectious disease research", # Antimicrobial/Stewardship "Antimicrobial Agents and Chemotherapy": "Laboratory and clinical antimicrobial research", "Journal of Antimicrobial Chemotherapy": "Clinical antimicrobial research and stewardship", "International Journal of Antimicrobial Agents": "Clinical and laboratory antimicrobial studies", "Antibiotics": "Comprehensive antibiotic research from bench to bedside", "Journal of Global Antimicrobial Resistance": "Global surveillance and resistance research", "Antimicrobial Resistance & Infection Control": "Prevention and control of antimicrobial resistance", # Infection Prevention "Infection Control and Hospital Epidemiology": "Healthcare epidemiology and infection prevention", "Journal of Hospital Infection": "Hospital infection control and prevention strategies", "American Journal of Infection Control": "Evidence-based infection prevention practices", "Journal of Infection Prevention": "Practical infection prevention for healthcare workers", # Microbiology "Nature Microbiology": "High-impact fundamental and applied microbiology research", "mBio": "Broad scope microbiology with rapid publication", "Journal of Clinical Microbiology": "Clinical microbiology and laboratory diagnostics", "Applied and Environmental Microbiology": "Applied microbiology and environmental research", "Frontiers in Microbiology": "Open access microbiology and infectious disease research", "Clinical Microbiology Reviews": "Comprehensive reviews in clinical microbiology", "Medical Mycology": "Medical and veterinary mycology research", # HIV/AIDS "Journal of Acquired Immune Deficiency Syndromes": "Clinical HIV/AIDS research and care", "AIDS": "Comprehensive HIV/AIDS research from basic to clinical", "The Lancet HIV": "High-impact HIV research with global health focus", "Journal of the International AIDS Society": "Global HIV research and advocacy", "HIV Medicine": "Clinical practice and research in HIV medicine", # Public Health "The Lancet Public Health": "High-impact public health research and policy", "American Journal of Public Health": "Public health research, policy, and practice", "American Journal of Epidemiology": "Epidemiological methods and population health", "Epidemiology and Infection": "Infectious disease epidemiology and control", "BMC Public Health": "Open access public health research platform", "Global Health Action": "Global health implementation and policy research", # Vaccines "Vaccine": "Comprehensive vaccine research from development to implementation", "Human Vaccines & Immunotherapeutics": "Vaccine research and immunotherapy development", "Vaccines": "Open access vaccine research and policy", "Expert Review of Vaccines": "Expert analysis of vaccine development and policy", "NPJ Vaccines": "High-impact vaccine research with novel approaches", # Travel Medicine "Journal of Travel Medicine": "Travel health, pre-travel advice, and tropical diseases", "Travel Medicine and Infectious Disease": "Travel-related infectious diseases and prevention", "Tropical Medicine & International Health": "Health research in tropical and resource-limited settings", "PLOS Neglected Tropical Diseases": "Research on neglected tropical diseases", # Wound Care "Wound Repair and Regeneration": "Basic and clinical research in wound healing", "International Wound Journal": "Clinical and research aspects of wound care", "Advances in Wound Care": "Innovative approaches to wound management", "Journal of Wound Care": "Evidence-based clinical wound care practice", # Pediatric ID "Pediatric Infectious Disease Journal": "Pediatric infectious diseases and immunizations", "Journal of the Pediatric Infectious Diseases Society": "Pediatric ID research and clinical practice", # STI "Sexually Transmitted Infections": "STI research, prevention, and public health", "Sexually Transmitted Diseases": "Clinical and epidemiological STD research", # Laboratory Medicine "Clinical Chemistry": "Clinical laboratory science and diagnostic medicine", "Journal of Clinical Laboratory Analysis": "Laboratory medicine and diagnostic methods", "Clinical Microbiology and Infection": "Clinical microbiology and infectious diseases", # One Health "One Health": "Interdisciplinary research connecting human, animal, and environmental health", "EcoHealth": "Ecosystem approaches to health and disease", # General Medical "The Lancet": "High-impact clinical research with global reach", "New England Journal of Medicine": "Premier clinical research and medical advances", "JAMA": "Clinical research, public health, and medical education", "Nature Medicine": "Translational and clinical medical research", # Open Access "PLOS ONE": "Rigorous science across all disciplines with open access", "PLOS Medicine": "Open access clinical and public health research", "PLOS Pathogens": "Open access research on pathogenic organisms", "Scientific Reports": "Multidisciplinary scientific research with open access", "Journal of Clinical Medicine": "Clinical research across medical specialties", # Regional "Journal of Infection and Chemotherapy": "Infectious diseases with Asian perspective", "Brazilian Journal of Infectious Diseases": "Infectious diseases in Latin America", "Infection and Drug Resistance": "Drug resistance research and clinical implications", # Implementation Science "Implementation Science": "Research on implementing evidence-based practices", "Health Policy and Planning": "Health systems research and policy implementation", "Journal of Hospital Medicine": "Hospital-based clinical research and quality improvement" } return scope_mapping.get(journal_name, "Peer-reviewed research in relevant medical fields") def _deduplicate_journals(self, journals: List[Dict[str, Any]]) -> List[Dict[str, Any]]: """ Remove duplicate journals and sort by relevance score. """ seen_journals = set() unique_journals = [] for journal in journals: journal_name = journal.get("name", "").lower() if journal_name not in seen_journals: seen_journals.add(journal_name) unique_journals.append(journal) # Sort by relevance score (descending) unique_journals.sort(key=lambda x: x.get("relevance_score", 0), reverse=True) return unique_journals def _format_journal_recommendations(self, journals: List[Dict[str, Any]], title: str, research_area: str) -> str: """ Format the journal recommendations for user display. """ if not journals: return f""" ## 📚 Journal Suggestions for: "{title}" **Research Area:** {research_area} ⚠️ **No specific journal matches found in search results.** ### General Recommendations: 1. **PLOS ONE** - Multidisciplinary open access journal 2. **BMC Infectious Diseases** - Open access infectious disease research 3. **Frontiers in Microbiology** - Open access microbiology research 4. **Journal of Clinical Medicine** - Broad clinical research scope 5. **Microorganisms** - General microbiology and infectious agents 💡 **Tip:** Consider refining your search terms or consulting journal finder tools from major publishers like Elsevier, Springer, or Wiley. """ result = f""" ## 📚 Journal Suggestions for: "{title}" **Research Area:** {research_area} ### 🎯 Recommended Journals (Ranked by Relevance): """ for i, journal in enumerate(journals, 1): result += f""" **{i}. {journal['name']}** - **Publisher:** {journal['publisher']} - **Impact Factor:** {journal['impact_factor']} (approximate) - **Topics:** {journal['topics']} - **Scope:** {journal['scope']} - **Relevance Score:** {journal['relevance_score']:.1f}/1.0 --- """ result += """ ### 💡 Additional Tips: - Check each journal's recent publications to confirm fit - Review submission guidelines and formatting requirements - Consider open access policies and publication fees - Look at editorial board expertise alignment - Check typical review timelines for your research urgency ### 🔍 Further Research: - Use publisher journal finder tools (Elsevier, Springer, Wiley) - Check Journal Citation Reports for updated impact factors - Review journal social media and recent highlights - Consider preprint servers (bioRxiv, medRxiv) for rapid dissemination """ return result