William R. Hogan

Yi Guo

Hui Shao

J. Am. Medical Informatics Assoc., December, 2023

Clinical concept and relation extraction using prompt-based machine reading comprehension.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., August, 2023

A study of generative large language model for medical research and healthcare.

[BibT_eX]

[DOI]

Yi Guo

npj Digit. Medicine, 2023

Creating a Discipline-specific Commons for Infectious Disease Epidemiology.

[BibT_eX]

[DOI]

Alexander T. Loiacono

Terence Sperringer Jr.

Shawn T. Brown

CoRR, 2023

A Study of Generative Large Language Model for Medical Research and Healthcare.

[BibT_eX]

[DOI]

CoRR, 2023

Clinical Concept and Relation Extraction Using Prompt-based Machine Reading Comprehension.

[BibT_eX]

[DOI]

CoRR, 2023

Ontology of language, with applications to demographic data.

[BibT_eX]

[DOI]

Appl. Ontology, 2023

The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards.

[BibT_eX]

[DOI]

Proceedings of the Joint Ontology Workshops 2023 Episode IX: The Quebec Summer of Ontology co-located with the 13th International Conference on Formal Ontology in Information Systems (FOIS 2023), 2023

2022

A large language model for electronic health records.

[BibT_eX]

[DOI]

npj Digit. Medicine, 2022

The OneFlorida Data Trust: a centralized, translational research data infrastructure of statewide scope.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2022

A scoping review of semantic integration of health data and information.

[BibT_eX]

[DOI]

Int. J. Medical Informatics, 2022

Phenotype clustering in health care: A narrative review for clinicians.

[BibT_eX]

[DOI]

Tezcan Ozrazgat-Baslanti

Gilbert R. Upchurch Jr.

Azra Bihorac

Frontiers Artif. Intell., 2022

SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies.

[BibT_eX]

[DOI]

CoRR, 2022

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies.

[BibT_eX]

[DOI]

CoRR, 2022

GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records.

[BibT_eX]

[DOI]

CoRR, 2022

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, 2022

Integration of Biobanking Architecture with Genomics Data: Genomics Integrated Biobanking Ontology (GIBO).

[BibT_eX]

[DOI]

Proceedings of the Advances in Informatics, Management and Technology in Healthcare, 2022

Identify Cancer Patients at Risk for Heart Failure using Electronic Health Record and Genetic Data.

[BibT_eX]

[DOI]

Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

Impacts of Eligibility Criteria on Trial Participants' Age in Alzheimer's Disease Clinical Trials.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2022, 2022

2021

Exploring the feasibility of using real-world data from a large clinical data research network to simulate clinical trials of Alzheimer's disease.

[BibT_eX]

[DOI]

Fei Wang

npj Digit. Medicine, 2021

Extracting social determinants of health from electronic health records using natural language processing: a systematic review.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2021

Applications of artificial intelligence in drug development using real-world data.

[BibT_eX]

[DOI]

CoRR, 2021

Developing an Ontology for Social and Behavioral Determinants of Health.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

A realism-based approach to an ontological representation of symbiotic interactions.

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2020

Clinical concept extraction using transformers.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2020

Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting.

[BibT_eX]

[DOI]

Xi Yang

Ragnhildur I. Bjarnadottir

Ruogu Fang

J. Am. Medical Informatics Assoc., 2020

Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data.

[BibT_eX]

[DOI]

Tonatiuh Mendoza Viramontes

Tianchen Lyu

Alexander T. Loiacono

J. Am. Medical Informatics Assoc., 2020

Predicting in-hospital mortality of patients with febrile neutropenia using machine learning models.

[BibT_eX]

[DOI]

Int. J. Medical Informatics, 2020

Developing and Validating a Computable Phenotype for the Identification of Transgender and Gender Nonconforming Individuals and Subgroups.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2020, 2020

2019

A study of deep learning methods for de-identification of clinical notes in cross-institute settings.

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2019

Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers.

[BibT_eX]

[DOI]

Jonathan P. Bona

Mathias Brochhausen

BMC Bioinform., 2019

A Study of Deep Learning Methods for De-identification of Clinical Notes at Cross Institute Settings.

[BibT_eX]

[DOI]

Proceedings of the 2019 IEEE International Conference on Healthcare Informatics, 2019

Identifying Cancer Patients at Risk for Heart Failure Using Machine Learning Methods.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

Assessing the Validity of a a priori Patient-Trial Generalizability Score using Real-world Data from a Large Clinical Data Research Network: A Colorectal Cancer Clinical Trial Case Study.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

2018

OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system.

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2018

Introducing Hypertension FACT: Vital Sign Ontology Annotations in the Florida Annotated Corpus for Translational Science.

[BibT_eX]

[DOI]

Proceedings of the Thirty-First International Florida Artificial Intelligence Research Society Conference, 2018

Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2018, 2018

Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2018, 2018

2017

Towards a privacy preserving cohort discovery framework for clinical research networks.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2017

Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2017

The Building Blocks of Inter-operability.

[BibT_eX]

[DOI]

Appl. Clin. Inform., 2017

That Which we Call a Pediatrician Would by Any Other Name a Child Treat (or not).

[BibT_eX]

[DOI]

Amanda Hicks

Dharani K. Balasubramanian

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

Ontology of Cancer Related Social-Ecological Variables.

[BibT_eX]

[DOI]

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

OC-2-KB: A software pipeline to build an evidence-based obesity and cancer knowledge base.

[BibT_eX]

[DOI]

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Building an Obesity and Cancer Semantic Web Knowledge Base.

[BibT_eX]

[DOI]

Arturo Gonzalez-Izquierdo

Proceedings of the AMIA 2017, 2017

Implementing a Hash-based Privacy-Preserving Entity Resolution Tool in the OneFlorida Clinical Data Research Network.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

Comparing and Contrasting A Priori and A Posteriori Generalizability Assessment of Clinical Trials on Type 2 Diabetes Mellitus.

[BibT_eX]

[DOI]

Zhe He

Proceedings of the AMIA 2017, 2017

2016

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2016

Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis.

[BibT_eX]

[DOI]

Werner Ceusters

J. Biomed. Semant., 2016

The ontology of medically related social entities: recent developments.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2016

An accurate and precise representation of drug ingredients.

[BibT_eX]

[DOI]

Josh Hanna

J. Biomed. Semant., 2016

Adding Evidence Type Representation to DIDEO.

[BibT_eX]

[DOI]

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

A Semantic Web Representation of Entire Populations.

[BibT_eX]

[DOI]

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Examining Healthcare Utilization Patterns of Elderly and Middle-Aged Adults in the United States.

[BibT_eX]

[DOI]

Cilia E. Zayas

Zhe He

Jiawei Yuan

Mildred Maldonado-Molina

Proceedings of the Twenty-Ninth International Florida Artificial Intelligence Research Society Conference, 2016

Towards an obesity-cancer knowledge base: Biomedical entity identification and relation detection.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Assessing the comorbidity gap between clinical studies and prevalence in elderly patient populations.

[BibT_eX]

[DOI]

Proceedings of the 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics, 2016

2015

Formalizing Knowledge and Evidence about Potential Drug-drug Interactions.

[BibT_eX]

[DOI]

Proceedings of International Workshop on Biomedical Data Mining, 2015

An ontological analysis of diagnostic assertions in electronic healthcare records.

[BibT_eX]

[DOI]

Werner Ceusters

Proceedings of the International Conference on Biomedical Ontology, 2015

Mining Twitter as a First Step toward Assessing the Adequacy of Gender Identification Terms on Intake Forms.

[BibT_eX]

[DOI]

Amanda Hicks

Michael W. Rutherford

Proceedings of the AMIA 2015, 2015

2014

Social network analysis of biomedical research collaboration networks in a CTSA institution.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2014

A Novel Representation of Terms Related to Infectious Disease Epidemiology for Epidemic Modeling: The Apollo Structured Vocabulary and Pre-existing Representations.

[BibT_eX]

[DOI]

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

2013

Evidence of community structure in Biomedical Research Grant Collaborations.

[BibT_eX]

[DOI]

Radhakrishnan Nagarajan

Alex T. Kalinka

J. Biomed. Informatics, 2013

Building a drug ontology based on RxNorm and other sources.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2013

Developing a semantically rich ontology for the biobank-administration domain.

[BibT_eX]

[DOI]

Roxana Merino-Martinez

J. Biomed. Semant., 2013

The Core Clinical Protocol Ontology (C2PO): A Realist Ontology for Representing the Recommendations within Clinical Guidelines.

[BibT_eX]

[DOI]

Proceedings of the MEDINFO 2013, 2013

Towards a Consistent and Scientifically Accurate Drug Ontology.

[BibT_eX]

[DOI]

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Maintaining the Drug Ontology: an Open-source, Structured Product Label API for the JVM.

[BibT_eX]

[DOI]

Roger A. Hall

Josh Hanna

Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th, 2013

A Demonstration of Entity Identity Information Management Applied to Demographic Data in a Referent Tracking System.

[BibT_eX]

[DOI]

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Understanding biomedicai research collaborations through social network analysis: A case study.

[BibT_eX]

[DOI]

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Apollo: Giving application developers a single point of access to public health models using structured vocabularies and Web services.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2013, 2013

2012

Simplifying MIREOT; a MIREOT Protege Plugin.

[BibT_eX]

[DOI]

Proceedings of the ISWC 2012 Posters & Demonstrations Track, 2012

2011

Natural Language Processing methods and systems for biomedical ontology learning.

[BibT_eX]

[DOI]

Kaihong Liu

Rebecca S. Crowley

J. Biomed. Informatics, 2011

Towards an ontological theory of substance intolerance and hypersensitivity.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2011

Representing Local Identifiers in a Referent-Tracking System.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Representing the Reality Underlying Demographic Data.

[BibT_eX]

[DOI]

Swetha Garimalla

Shariq A. Tariq

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2009

Mining aggregates of over-the-counter products for syndromic surveillance.

[BibT_eX]

[DOI]

Pattern Recognit. Lett., 2009

Measuring the effect of commuting on the performance of the Bayesian Aerosol Release Detector.

[BibT_eX]

[DOI]

Aurel Cami

BMC Medical Informatics Decis. Mak., 2009

Knowledge-based variable selection for learning rules from proteomic data.

[BibT_eX]

[DOI]

Jonathan L. Lustgarten

Shyam Visweswaran

Robert P. Bowser

Vanathi Gopalakrishnan

BMC Bioinform., 2009

2008

EPO-KB: a <i>searchable</i> knowledge base of biomarker to protein links.

[BibT_eX]

[DOI]

Jonathan L. Lustgarten

Chad Kimmel

Henrik Ryberg

Bioinform., 2008

A Temporal Extension of the Bayesian Aerosol Release Detector.

[BibT_eX]

[DOI]

Xiaohui Kong

Proceedings of the Biosurveillance and Biosecurity, International Workshop, 2008

Integrating a Commuting Model with the Bayesian Aerosol Release Detector.

[BibT_eX]

[DOI]

Aurel Cami

Proceedings of the Biosurveillance and Biosecurity, International Workshop, 2008

2007

Unsupervised clustering of over-the-counter healthcare products into product categories.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2007

2005

Algorithms for rapid outbreak detection: a research synthesis.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2005

A Multivariate Procedure for Identifying Correlations between Diagnoses and Over-the-counter Products from Historical Datasets.

[BibT_eX]

[DOI]

Ran Li

Proceedings of the AMIA 2005, 2005

An Evaluation of Three Policies for Updating Product Categories in the National Retail Data Monitor.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2005, 2005

2004

Bayesian Biosurveillance of Disease Outbreaks.

[BibT_eX]

[DOI]

Proceedings of the UAI '04, 2004

Analysis of Web Access Logs for Surveillance of Influenza.

[BibT_eX]

[DOI]

Proceedings of the MEDINFO 2004, 2004

2003

Application of Information Technology: Design of a National Retail Data Monitor for Public Health Surveillance.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2003

Research Paper: Detection of Pediatric Respiratory and Diarrheal Outbreaks from Sales of Over-the-counter Electrolyte Products.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2003

Detection of Outbreaks from Time Series Data Using Wavelet Transform.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2003, 2003

A Framework for Infection Control Surveillance Using Association Rules.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2003, 2003

Detection of Pediatric Respiratory and Gastrointestinal Outbreaks from Free-Text Chief Complaints.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2003, 2003

Telephone Triage: A Timely Data Source for Surveillance of Influenza-like Diseases.

[BibT_eX]

[DOI]

Jeremy U. Espino

Proceedings of the AMIA 2003, 2003

2002

Experience with Message Format and Code Set Standards for Early Warning Public Health Surveillance Systems.

[BibT_eX]

[DOI]

Fu-Chiang Tsui

Proceedings of the AMIA 2002, 2002

1999

A feasibility study of two methods for end-user configuration of a clinical event monitor.

[BibT_eX]

[DOI]

Proceedings of the AMIA 1999, 1999

The use of an explanation algorithm in a clinical event monitor.

[BibT_eX]

[DOI]

Proceedings of the AMIA 1999, 1999

1998

Preferences of interns and residents for E-mail, paging, or traditional methods for the delivery of different types of clinical information.

[BibT_eX]

[DOI]

Proceedings of the AMIA 1998, 1998

Optimal use of communication channels in clinical event monitoring.

[BibT_eX]

[DOI]

Proceedings of the AMIA 1998, 1998

Mobile workers in healthcare and their information needs: are 2-way pagers the answer?

[BibT_eX]

[DOI]

Proceedings of the AMIA 1998, 1998

1997

Review: Accuracy of Data in Computer-based Patient Records.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 1997

Clinical event monitoring at the University of Pittsburgh.

[BibT_eX]

[DOI]

Proceedings of the AMIA 1997, 1997

1996

Research Paper: The Accuracy of Medication Data in an Outpatient Electronic Medical Record.

[BibT_eX]

[DOI]