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

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

Using Ontologies to Enhance Data on Intimate Partner Violence.

[BibT_eX]

[DOI]

S. Clint Dowland

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

An Ontological Representation of Money with a View Toward Economic Determinants of Health.

[BibT_eX]

[DOI]

Matthew Diller

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 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]