You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: ["HealthCareActivity", "InjuryOrPoisoning", "BodySubstance", "IntellectualProduct", "AnatomicalStructure", "SpatialConcept", "Chemical", "Bacterium", "MedicalDevice", "Organization", "BiomedicalOccupationOrDiscipline", "Finding", "BiologicFunction", "Virus", "ResearchActivity", "ClinicalAttribute", "PopulationGroup", "Eukaryote", "BodySystem", "Food", "ProfessionalOrOccupationalGroup"].

Please return the output as a JSON object of the format: {"Virus": ["HIV", ...], "Bacterium": ["MRSA", ...], "AnatomicalStructure": ["Lung", ...], "BodySystem": ["CNS", ...], "BodySubstance": ["Serum", ...], "Finding": ["Headache", ...], "InjuryOrPoisoning": ["Fracture", ...], "BiologicFunction": ["Death", ...], "HealthCareActivity": ["Biopsy", ...], "ResearchActivity": ["Clinical trial", ...], "MedicalDevice": ["Lenses", ...], "SpatialConcept": ["Camps", ...], "BiomedicalOccupationOrDiscipline": ["Forensic medicine", ...], "Organization": ["WHO", ...], "ProfessionalOrOccupationalGroup": ["Provider", ...], "PopulationGroup": ["Swimmers", ...], "Chemical": ["Gold", ...], "Food": ["Rice", ...], "IntellectualProduct": ["RPAM", ...], "ClinicalAttribute": ["Biomarker", ...], "Eukaryote": ["Dogs", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].

Only output the JSON object and do not include any additional text.

Abstract:

Enhancing Comparative Effectiveness Research With Automated Pediatric Pneumonia Detection in a Multi-Institutional Clinical Repository: A PHIS + Pilot Study Community-acquired pneumonia is a leading cause of pediatric morbidity. Administrative data are often used to conduct comparative effectiveness research (CER) with sufficient sample sizes to enhance detection of important outcomes. However, such studies are prone to misclassification errors because of the variable accuracy of discharge diagnosis codes. The aim of this study was to develop an automated, scalable, and accurate method to determine the presence or absence of pneumonia in children using chest imaging reports. The multi-institutional PHIS + clinical repository was developed to support pediatric CER by expanding an administrative database of children's hospitals with detailed clinical data. To develop a scalable approach to find patients with bacterial pneumonia more accurately, we developed a Natural Language Processing (NLP) application to extract relevant information from chest diagnostic imaging reports. Domain experts established a reference standard by manually annotating 282 reports to train and then test the NLP application. Findings of pleural effusion, pulmonary infiltrate, and pneumonia were automatically extracted from the reports and then used to automatically classify whether a report was consistent with bacterial pneumonia. Compared with the annotated diagnostic imaging reports reference standard, the most accurate implementation of machine learning algorithms in our NLP application allowed extracting relevant findings with a sensitivity of .939 and a positive predictive value of .925. It allowed classifying reports with a sensitivity of .71, a positive predictive value of .86, and a specificity of .962. When compared with each of the domain experts manually annotating these reports, the NLP application allowed for significantly higher sensitivity (.71 vs .527) and similar positive predictive value and specificity. NLP -based pneumonia information extraction of pediatric diagnostic imaging reports performed better than domain experts in this pilot study. NLP is an efficient method to extract information from a large collection of imaging reports to facilitate CER.
{"AnatomicalStructure": [], "Bacterium": [], "BiologicFunction": ["Community-acquired pneumonia", "Pneumonia", "pleural effusion", "pneumonia", "bacterial pneumonia"], "BiomedicalOccupationOrDiscipline": [], "BodySubstance": [], "BodySystem": [], "Chemical": [], "ClinicalAttribute": [], "Eukaryote": [], "Finding": ["find", "discharge diagnosis", "positive", "presence", "detection", "pulmonary infiltrate"], "Food": [], "HealthCareActivity": ["chest imaging", "chest diagnostic imaging", "Detection", "diagnostic imaging"], "InjuryOrPoisoning": [], "IntellectualProduct": ["imaging reports", "database", "codes", "classifying", "PHIS", "classify", "reports", "algorithms", "report", "method"], "MedicalDevice": [], "Organization": ["Multi-Institutional", "children\u0027s hospitals", "multi-institutional"], "PopulationGroup": [], "ProfessionalOrOccupationalGroup": ["experts"], "ResearchActivity": ["CER", "comparative effectiveness research", "Comparative Effectiveness Research", "pilot study", "Pilot Study"], "SpatialConcept": [], "Virus": []}