List of works by Christopher G. Chute

A Collaborative Framework for Representation and Harmonization of Clinical Study Data Elements Using Semantic MediaWiki.

scientific article

A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome

scientific article (publication date: 2013)

A NOVEL GENOMIC SUSCEPTIBILITY LOCUS FOR PERIPHERAL ARTERIAL DISEASE ON CHROMOSOME 12

A Pilot Study on Modeling of Diagnostic Criteria Using OWL and SWRL.

scientific article published on January 2015

A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials

scientific article published on 25 March 2015

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution

scientific article published on January 2015

A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project

scientific article published on 14 November 2014

A brief Patient-Reported Outcomes Quality of Life (PROQOL) instrument to improve patient care

scientific article

A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury

scientific article published on 09 July 2013

A common type system for clinical natural language processing

scientific article published on 3 January 2013

A comparative study of supervised learning as applied to acronym expansion in clinical reports

scientific article published on January 2006

A conceptual model for translating omic data into clinical action

scientific article

A corpus driven approach applying the "frame semantic" method for modeling functional status terminology.

scientific article published on January 2004

A data-driven approach for extracting "the most specific term" for ontology development

scientific article

A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects

scientific article published on 12 September 2013

A genome-wide association study of red blood cell traits using the electronic medical record.

scientific article

A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes

scientific article

A hybrid approach to determining modification of clinical diagnoses.

scientific article published on January 2006

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data

scientific article

A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers

scientific article published in Nature Communications

A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept.

scientific article published in August 2003

A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis

scientific article

ADEpedia 2.0: Integration of Normalized Adverse Drug Events (ADEs) Knowledge from the UMLS.

scientific article published on 18 March 2013

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology

scientific article published on 22 October 2011

Abbreviation and acronym disambiguation in clinical discourse.

scientific article published on January 2005

Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources

scientific article (publication date: 12 August 2008)

Adverse Drug Event-based Stratification of Tumor Mutations: A Case Study of Breast Cancer Patients Receiving Aromatase Inhibitors

scientific article published on 14 November 2014

Adverse Drug Events-based Tumor Stratification for Ovarian Cancer Patients Receiving Platinum Therapy.

scientific article published on 23 March 2015

Agreement between patient-reported symptoms and their documentation in the medical record

scientific article published on August 2008

An OWL meta-ontology for representing the Clinical Element Model

scientific article published on 22 October 2011

An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records.

scientific article

An automated approach for ranking journals to help in clinician decision support

scientific article published on 14 November 2014

An evaluation of unmediated versus mediated retrieval services.

scientific article

An information extraction framework for cohort identification using electronic health records

scientific article published on 18 March 2013

Analysis of cross-institutional medication description patterns in clinical narratives

scientific article published on 24 June 2013

Analyzing categorical information in two publicly available drug terminologies: RxNorm and NDF-RT

scientific article

Analyzing the heterogeneity and complexity of Electronic Health Record oriented phenotyping algorithms.

scientific article published on 22 October 2011

Application of a temporal reasoning framework tool in analysis of medical device adverse events.

scientific article published on 22 October 2011

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

scientific article (publication date: 17 December 2012)

Auditing the semantic completeness of SNOMED CT using formal concept analysis

scientific article published on 24 October 2008

Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record

scientific article

Automated recommendation for cervical cancer screening and surveillance

scientific article

Automating the assignment of diagnosis codes to patient encounters using example-based and machine learning techniques

scientific article

Biosurveillance, classification, and semantic health technologies

scientific article published in March 2008

Building Standardized Semantic Web RESTful Services to Support ICD-11 Revision ⬇️

Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies ⬇️

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies

scientific article

Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project

scientific article

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies

scientific article

Building and evaluating annotated corpora for medical NLP systems

scientific article published on January 2006

CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives

scientific article published on 7 March 2011

CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives

scientific article

CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record

scientific article published on 03 July 2015

Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing

scientific article

Characterizing Long COVID: Deep Phenotype of a Complex Condition

scientific article published on 25 November 2021

Classification, Ontology, and Precision Medicine

Clinical Data: Sources and Types, Regulatory Constraints, Applications

scientific article published on 09 May 2019

Clinical element models in the SHARPn consortium.

scientific article

Coding patient information, reimbursement for care, and the ICD transition

scientific article published in July 2013

Commentary: nursing practice content standards

scientific article published on 01 September 2008

Comorbidity Characterization Among eMERGE Institutions: A Pilot Evaluation with the Johns Hopkins Adjusted Clinical Groups® System.

scientific article published on 6 May 2019

Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG.

scientific article

Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate

scientific article

Content coverage of SNOMED-CT toward the ICU nursing flowsheets and the acuity indicators

scientific article published on January 2006

Creating a purpose-driven learning and improving health system: The Johns Hopkins Medicine quality and safety experience

scientific article published on 15 December 2016

Cross-terminology mapping challenges: a demonstration using medication terminological systems

scientific article

Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data

scientific article

Dependency Parser-based Negation Detection in Clinical Narratives

scientific article published on 19 March 2012

Desiderata for computable representations of electronic health records-driven phenotype algorithms

scientific article

Detecting Associations between Major Depressive Disorder Treatment and Essential Hypertension using Electronic Health Records

scientific article published on 7 April 2014

Developing a Standards-Based Information Model for Representing Computable Diagnostic Criteria: A Feasibility Study of the NQF Quality Data Model.

scientific article

Developing a corpus of clinical notes manually annotated for part-of-speech

scientific article published on 19 September 2005

Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution

scientific article

Developing a modular architecture for creation of rule-based clinical diagnostic criteria

scientific article published on 21 October 2016

Developing a section labeler for clinical documents

scientific article published on 14 November 2014

Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration

scientific article published on 22 January 2022

Developing the surveillance algorithm for detection of failure to recognize and treat severe sepsis

scientific article published on 06 January 2015

Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL.

scientific article published on 29 May 2013

Discovering associations among diagnosis groups using topic modeling

scientific article published on 7 April 2014

Discovering peripheral arterial disease cases from radiology notes using natural language processing

scientific article

Domain-specific language models and lexicons for tagging

scientific article published on 02 April 2005

Drug Normalization for Cancer Therapeutic and Druggable Genome Target Discovery.

scientific article published on 25 March 2015

Drug repositioning candidates identified using in-silico quasi-quantum molecular simulation demonstrate reduced COVID-19 mortality in 1.5M patient records

scholarly article by Joy Alamgir published in 2021

Drug side effect extraction from clinical narratives of psychiatry and psychology patients

scientific article published on 21 September 2011

EHR based Genetic Testing Knowledge Base (iGTKB) Development

scientific article published on 25 November 2015

Electronic medical records for clinical research: application to the identification of heart failure.

scientific article published on June 2007

Electronic medical records for genetic research: results of the eMERGE consortium

scientific article published on April 2011

Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example

scientific article published on 01 October 2018

Erratum to “Cross-terminology mapping challenges: A demonstration using medication terminological systems” [J. Biomed. Inform. (2012) 613–625]

scholarly article published in Journal of Biomedical Informatics

Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects.

scientific article

Evaluation of RxNorm for Medication Clinical Decision Support

scientific article published on 14 November 2014

Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging Web ontology language (OWL) and cheminformatics approaches

scientific article published on January 2014

Fast Healthcare Interoperability Resources (FHIR) as a Meta Model to Integrate Common Data Models: Development of a Tool and Quantitative Validation Study

scientific article published on 16 October 2019

Feature engineering with clinical expert knowledge: A case study assessment of machine learning model complexity and performance

scientific article published on 23 April 2020

Formalizing ICD coding rules using Formal Concept Analysis

scientific article published on 21 February 2009

Formalizing the International Classification of Functioning, Disability, and Health (ICF) using Formal Concept Analysis (FCA).

scientific article published on 11 October 2007

From clinical records to regulatory reporting: formal terminologies as foundation

scientific article

Further revamping VA's NDF-RT drug terminology for clinical research

scientific article published on 17 March 2011

Generality and reuse in a common type system for clinical natural language processing

article published in 2011

Genetic Loci implicated in erythroid differentiation and cell cycle regulation are associated with red blood cell traits

scientific article published on May 2012

Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network

scientific article

Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk

scientific article published on 05 March 2013

Genome-wide study of resistant hypertension identified from electronic health records

scientific article

Genomic medicine, health information technology, and patient care

scientific article published on April 2013

Granular Quality Reporting for Cervical Cytology Testing

scientific article published on 25 March 2015

Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study

scientific article

Health data use, stewardship, and governance: ongoing gaps and challenges: a report from AMIA's 2012 Health Policy Meeting

scientific article

Health information technology data standards get down to business: maturation within domains and the emergence of interoperability

scientific article published on 16 May 2015

ICD-11 and SNOMED CT Common Ontology: circulatory system

scientific article published on January 2014

Identification of unique venous thromboembolism-susceptibility variants in African-Americans.

scientific article

Identifying Abdominal Aortic Aneurysm Cases and Controls using Natural Language Processing of Radiology Reports

scientific article published on 18 March 2013

Impact of data fragmentation across healthcare centers on the accuracy of a high-throughput clinical phenotyping algorithm for specifying subjects with type 2 diabetes mellitus

scientific article

Incorporating expert terminology and disease risk factors into consumer health vocabularies

scientific article published on January 2013

Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results.

scientific article published on January 2012

Interface Terminologies, Reference Terminologies and Aggregation Terminologies: A Strategy for Better Integration

scientific article published in January 2017

Investigating the Genetic Architecture of the PR Interval Using Clinical Phenotypes

scientific article published on April 2017

Invited commentary: Observational research in the age of the electronic health record

scientific article published on 30 January 2014

Isosemantic rendering of clinical information using formal ontologies and RDF.

scientific article published on January 2013

Keeping raw data in context

scientific article published in February 2009

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease ⬇️

scientific article published on September 1, 2010

LexGrid Editor: Terminology Authoring for the Lexical Grid

LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime

scientific article

LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies. ⬇️

scientific article

LexValueSets: an approach for context-driven value sets extraction

scientific article (publication date: 6 November 2008)

Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience

scientific article

Maximum entropy modeling for mining patient medication status from free text

scientific article published on January 2002

Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels

scientific article

Mayo clinic NLP system for patient smoking status identification

scientific article

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

scientific article

Measures of semantic similarity and relatedness in the biomedical domain

scientific article published on 10 June 2006

MedXN: an open source medication extraction and normalization tool for clinical text

scientific article

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying

scientific article (publication date: 2013)

Mining severe drug-drug interaction adverse events using Semantic Web technologies: a case study

scientific article published on 25 March 2015

Mining the human phenome using semantic web technologies: a case study for Type 2 Diabetes

scientific article (publication date: 2012)

Modeling and executing electronic health records driven phenotyping algorithms using the NQF Quality Data Model and JBoss® Drools Engine

scientific article

Modeling guidelines for integration into clinical workflow

scientific article published on 01 January 2004

Modular Ontology Techniques and their Applications in the Biomedical Domain

scientific article (publication date: 5 August 2008)

Mondo: Unifying diseases for the world, by the world

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

scientific article

Natural History of Prostatism

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network

scientific article

New filovirus disease classification and nomenclature

article

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

scientific article

On beyond Gruber: “Ontologies” in today’s biomedical information systems and the limits of OWL

scientific article

Ontology-based Temporal Analysis for Medical Device Adverse Event - A Use Case Study on Late Stent Thrombosis ⬇️

scholarly article by Kimberly Clark et al published 7 January 2014 in Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis

scientific article published on 20 December 2012

Open Source Clinical NLP - More than Any Single System

scientific article published on 7 April 2014

Overview of ICD-11 architecture and structure

publication published on 16 May 2022

PharmGKB Drug Data Normalization with NDF-RT.

scientific article

Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index

scientific article

Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER.

scientific article published on 21 September 2016

Practical considerations in genomic decision support: The eMERGE experience

scientific article

Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups

scientific article published on 01 May 2020

Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol

scientific article

Probing the Virtual Proteome to Identify Novel Disease Biomarkers

scientific article published on 01 November 2018

Profiling structured product labeling with NDF-RT and RxNorm

scientific article published on 20 December 2012

Proposed SKOS Extensions for BioPortal Terminology Services

Prospective recruitment of patients with congestive heart failure using an ad-hoc binary classifier.

scientific article

Psychological assessment instruments: a coverage analysis using SNOMED CT, LOINC and QS terminology

scientific article

Public health, data standards, and vocabulary: crucial infrastructure for reliable public health surveillance

scientific article

Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach

scientific article

Quality evaluation of cancer study Common Data Elements using the UMLS Semantic Network

scientific article

Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups

scientific article

Representing lexical components of medical terminologies in OWL

scientific article

Representing the ClaML-based ICD10 in LexGrid terminology model.

scientific article

SMART-on-FHIR implemented over i2b2

scientific article

Semantator: annotating clinical narratives with semantic web ontologies.

scientific article

Semantator: semantic annotator for converting biomedical text to linked data

scientific article

Semantic Alignment between ICD-11 and SNOMED CT.

scientific article published on January 2015

Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery: Supplementary materials

article

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

article

Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon

scientific article published on 30 October 2019

Sharing ontology between ICD 11 and SNOMED CT will enable seamless re-use and semantic interoperability

scientific article published on January 2013

Simplifying complex clinical element models to encourage adoption

scientific article published on 07 April 2014

Some experiences and opportunities for big data in translational research.

scientific article

Standardized drug and pharmacological class network construction

scientific article published on January 2013

Survey of modular ontology techniques and their applications in the biomedical domain

scientific article (publication date: August 2009)

Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs

scientific article

Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

scientific article

Terminology access methods leveraging LDAP resources.

scientific article published in January 2004

Terminology representation guidelines for biomedical ontologies in the semantic web notations

scientific article published on 28 September 2012

Testing the generalizability of the ISO model for nursing diagnoses

scientific article

The 2018 fellow cohort of the American College of Medical Informatics

scientific article published on 01 October 2019

The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study

scientific article

The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future

scientific article (publication date: October 2013)

The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data

scientific article

The Human Phenotype Ontology in 2021

scientific article published on 02 December 2020

The Human Phenotype Ontology in 2024: phenotypes around the world

scientific article published in 2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

The National Center for Biomedical Ontology

scientific article

The Open Terminology Services (OTS) project.

scientific article

The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation

scientific article published on 19 March 2013

The Pluripotent Rendering of Clinical Data for Precision Medicine

scientific article published in January 2017

The Return of Actionable Variants Empirical (RAVE) Study, a Mayo Clinic Genomic Medicine Implementation Study: Design and Initial Results

scientific article published on 01 November 2018

The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities.

scientific article

The Southeastern Minnesota Beacon Project for Community-driven Health Information Technology: Origins, Achievements, and Legacy

scientific article

The absence of longitudinal data limits the accuracy of high-throughput clinical phenotyping for identifying type 2 diabetes mellitus subjects

scientific article

The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies

scientific article (publication date: 26 January 2011)

The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype

scientific article published on 08 October 2018

The first step toward data reuse: disambiguating concept representation of the locally developed ICU nursing flowsheets

scientific article

The horizontal and vertical nature of patient phenotype retrieval: new directions for clinical text processing

scientific article

The rendering of human phenotype and rare diseases in ICD-11.

scientific article published on 29 March 2018

There are important reasons for delaying implementation of the new ICD-10 coding system

scientific article

Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques

scientific article published in ISWC 2010

Time-related patient data retrieval for the case studies from the pharmacogenomics research network

scientific article

Toward a Harmonized WHO Family of International Classifications Content Model

scientific article published on 01 June 2020

Toward near real-time acuity estimation: a feasibility study.

scientific article

Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies.

scientific article

Towards a framework for developing semantic relatedness reference standards ⬇️

scientific article published on October 31, 2010

Towards a semantic lexicon for clinical natural language processing

scientific article published on 3 November 2012

Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes

scientific article published on 10 February 2015

Trends in mastectomy rates at the Mayo Clinic Rochester: effect of surgical year and preoperative magnetic resonance imaging

scientific article published on 27 July 2009

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis

scientific article

Use of Hydroxychloroquine, Remdesivir, and Dexamethasone Among Adults Hospitalized With COVID-19 in the United States : A Retrospective Cohort Study

publication published on 17 August 2021

Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study

scientific article published on 19 November 2011

Using RxNorm and NDF-RT to classify medication data extracted from electronic health records: experiences from the Rochester Epidemiology Project

scientific article

Using Semantic Web Techologies for the Generation of Domain Templates to Support Clinical Study Meta-Data ⬇️

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards

scientific article published on 3 March 2016

Using Semantic Web technology to support icd-11 textual definitions authoring

scientific article (publication date: 21 April 2013)

Using association rule mining for phenotype extraction from electronic health records

scientific article published on 18 March 2013

Using clinical element models for pharmacogenomic study data standardization

scientific article

Using compound codes for automatic classification of clinical diagnoses.

scientific article published in January 2004

Using linked data for mining drug-drug interactions in electronic health records

scientific article (publication date: 2013)

Using semantic web technologies for cohort identification from electronic health records for clinical research

scientific article (publication date: 2012)

Validation and discovery of genotype-phenotype associations in chronic diseases using linked data

scientific article

Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network

scientific article published on 26 March 2013

Value of Genetics-informed Drug Dosing Guidance in Pregnant Women: A Needs Assessment with Obstetric Healthcare Providers at Johns Hopkins.

scientific article published in January 2017

Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies

scientific article

What's in a class? Lessons learnt from the ICD - SNOMED CT harmonisation

scientific article published on January 2014

Word sense disambiguation across two domains: biomedical literature and clinical notes

scientific article

caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.

scientific article

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