Christopher G. Chute
A5060390916- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Natural Language Processing Techniques
- Electronic Health Records Systems
- COVID-19 Clinical Research Studies
- Topic Modeling
- Genomics and Rare Diseases
- Long-Term Effects of COVID-19
- Machine Learning in Healthcare
- Medical Coding and Health Information
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Genetic Associations and Epidemiology
- linguistics and terminology studies
- Urinary Bladder and Prostate Research
- Clinical practice guidelines implementation
- Artificial Intelligence in Healthcare
- Prostate Cancer Diagnosis and Treatment
- Computational Drug Discovery Methods
- Pelvic floor disorders treatments
- COVID-19 and healthcare impacts
- Chronic Disease Management Strategies
- Ethics in Clinical Research
- Data Quality and Management
- Health Sciences Research and Education
Johns Hopkins University
2016-2025
Johns Hopkins Medicine
2016-2025
Collaborative Research Group
2024
Cohort (United Kingdom)
2024
University of Alabama at Birmingham
2021-2022
University of Baltimore
2022
Florida International University
2022
University of Colorado Anschutz Medical Campus
2022
Hughston Clinic
2022
Creative Commons
2022
We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. describe our system, the Text Analysis Knowledge Extraction System (cTAKES), released at http://www.ohnlp.org. The cTAKES builds on existing technologies—the Unstructured Information Management Architecture framework OpenNLP toolkit. Its components, specifically trained domain, create rich linguistic semantic annotations. Performance of...
Recent epidemiologic evidence indicates an association between fat distribution and many diseases. To assess the validity of circumference measurements obtained by self-report, authors analyzed data from 123 men aged 40-75 years 140 women 41-65 years, drawn two large ongoing prospective studies. On mailed questionnaires, subjects were asked to measure record their weight waist hip circumferences. These compared with standardized taken approximately six months apart technicians who visited...
Abstract The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard describe and computationally analyze phenotypic abnormalities found human disease. HPO is now worldwide for phenotype exchange. has grown steadily since its inception due considerable contributions from clinical experts researchers diverse range of disciplines. Here, we present recent major extensions the neurology, nephrology, immunology, pulmonology, newborn...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical that provides access via Web services browsers developed in OWL, RDF, OBO format Protégé frames. functionality includes the ability browse, search visualize ontologies. The interface also facilitates community-based participation evaluation...
To establish the age-specific prevalence of urinary symptoms among a community-based cohort men, randomly selected sample men were screened and invited to participate in longitudinal survey symptoms. The population Olmsted County, Minnesota, as enumerated by Rochester Epidemiology Project, formed sampling base for this study. Men between 40 79 years old with no history prostate or other urological surgery, who also free conditions associated neurogenic bladder participate. A previously...
Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical are abundant, these largely inaccessible to outside researchers. Statistical, machine learning, causal analyses most successful with large-scale beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level from many centers.The...
A unified model for text categorization and retrieval is introduced. We use a training set of manually categorized documents to learn word-category associations, these associations predict the categories arbitrary documents. Similarly, we queries their related obtain empirical between query words indexing terms documents, queries. Linear Least Squares Fit (LLSF) technique employed estimate likelihood associations. Document collections from MEDLINE database Mayo patient records are used...
Genetic studies require precise phenotype definitions, but electronic medical record (EMR) data are recorded inconsistently and in a variety of formats.To present lessons learned about validation EMR-based phenotypes from the Electronic Medical Records Genomics (eMERGE) studies.The eMERGE network created validated 13 EMR-derived algorithms. Network sites Group Health, Marshfield Clinic, Mayo Northwestern University, Vanderbilt University.By validating we that: (1) multisite improves...
Recent changes have occurred in the presurgical planning for breast cancer, including introduction of preoperative magnetic resonance imaging (MRI). We sought to analyze trends mastectomy rates and relationship MRI surgical year at Mayo Clinic, Rochester, MN.We identified 5,405 patients who underwent surgery between 1997 2006. Patients undergoing were from a prospective database. Trends rate association with type analyzed. Multiple logistic regression was used assess effect on type, while...
Clinical data captured in electronic medical records accurately identify cases and controls for genome-wide association studies.
Genome-wide association studies (GWAS) require high specificity and large numbers of subjects to identify genotype-phenotype correlations accurately. The aim this study was type 2 diabetes (T2D) cases controls for a GWAS, using data captured through routine clinical care across five institutions different electronic medical record (EMR) systems.An algorithm developed T2D based on combination diagnoses, medications, laboratory results. performance the validated at three participating compared...
The National Center for Biomedical Ontology is now in its seventh year. goals of this Computing are to: create and maintain a repository biomedical ontologies terminologies; build tools web services to enable the use terminologies clinical translational research; educate their trainees scientific community broadly about ontology ontology-based technology best practices; collaborate with variety groups who develop biomedicine. centerpiece web-based resource known as BioPortal. BioPortal makes...
<h3>Importance</h3> Persons with immune dysfunction have a higher risk for severe COVID-19 outcomes. However, these patients were largely excluded from SARS-CoV-2 vaccine clinical trials, creating large evidence gap. <h3>Objective</h3> To identify the incidence rate and ratio (IRR) breakthrough infection after vaccination among persons or without dysfunction. <h3>Design, Setting, Participants</h3> This retrospective cohort study analyzed data National COVID Cohort Collaborative (N3C),...
We describe here the design and initial implementation of eMERGE-PGx project. eMERGE-PGx, a partnership Electronic Medical Records Genomics Network Pharmacogenomics Research Network, has three objectives: (i) to deploy PGRNseq, next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, nearly 9,000 patients likely be prescribed drugs interest 1- 3-year time frame across several clinical sites; (ii) integrate well-established clinically validated...
The National COVID Cohort Collaborative (N3C) is a centralized, harmonized, high-granularity electronic health record repository that the largest, most representative COVID-19 cohort to date. This multicenter data set can support robust evidence-based development of predictive and diagnostic tools inform clinical care policy.