Trends and opportunities in computable clinical phenotyping: A scoping review

Generalized and Transferable Patient Language Representation for Phenotyping with Limited Data

(2021) Yuqi Si et al.   JOURNAL OF BIOMEDICAL INFORMATICS

ACE: the Advanced Cohort Engine for searching longitudinal patient records

(2021) Alison Callahan et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Electronic phenotyping of health outcomes of interest using a linked claims-electronic health record database: Findings from a machine learning pilot project

(2021) Teresa B Gibson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Explainable Artificial Intelligence in High-Throughput Drug Repositioning for Subgroup Stratifications with Interventionable Potential

(2021) Zainab Al-Taie et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Ascertaining Framingham heart failure phenotype from inpatient electronic health record data using natural language processing: a multicentre Atherosclerosis Risk in Communities (ARIC) validation study

(2021) Carlton R Moore et al.   BMJ Open

Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study

(2021) Nansu Zong et al.   JMIR Medical Informatics

Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies

(2021) Danqing Xu et al.   npj Digital Medicine

Using a Multi-Institutional Pediatric Learning Health System to Identify Systemic Lupus Erythematosus and Lupus Nephritis

(2021) Scott E. Wenderfer et al.   Clinical Journal of the American Society of Nephrology

Emerging technologies and their impact on regulatory science

(2021) Elke Anklam et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Identifying cases of spinal cord injury or disease in a primary care electronic medical record database

(2021) John Shepherd et al.   JOURNAL OF SPINAL CORD MEDICINE

A methodology based on Trace-based clustering for patient phenotyping

(2021) Antonio Lopez-Martinez-Carrasco et al.   KNOWLEDGE-BASED SYSTEMS

Derivation and validation of a computable phenotype for acute decompensated heart failure in hospitalized patients

(2020) Rahul Kashyap et al.   BMC Medical Informatics and Decision Making

Computable Phenotype Implementation for a National, Multicenter Pragmatic Clinical Trial

(2020) Faraz S. Ahmad et al.  

A framework to build similarity-based cohorts for personalized treatment advice – a standardized, but flexible workflow with the R package SimBaCo

(2020) Lucas Wirbka et al.   PLoS One

Inferring multimodal latent topics from electronic health records

(2020) Yue Li et al.   Nature Communications

Precision and Personalized Medicine: How Genomic Approach Improves the Management of Cardiovascular and Neurodegenerative Disease

(2020) Oriana Strianese et al.   Genes

Rule-Based Cohort Definitions for Acute Respiratory Failure: Electronic Phenotyping Algorithm

(2020) Patrick Essay et al.   JMIR Medical Informatics

Characterizing the clinical and genetic spectrum of polycystic ovary syndrome in electronic health records

(2020) Ky’Era V Actkins et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Generative transfer learning for measuring plausibility of EHR diagnosis records

(2020) Hossein Estiri et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

EMR-Based Phenotyping of Ischemic Stroke Using Supervised Machine Learning and Text Mining Techniques

(2020) Sheng-Feng Sung et al.   IEEE Journal of Biomedical and Health Informatics

Developing and evaluating a pediatric asthma severity computable phenotype derived from electronic health records

(2020) Komal Peer et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Identifying Patient Phenotype Cohorts Using Prehospital Electronic Health Record Data

(2020) Rachel Stemerman et al.   Prehospital Emergency Care

Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms

(2019) April Jorge et al.   SEMINARS IN ARTHRITIS AND RHEUMATISM

Performance of a computable phenotype for identification of patients with diabetes within PCORnet: The Patient-Centered Clinical Research Network

(2019) Andrew D. Wiese et al.   PHARMACOEPIDEMIOLOGY AND DRUG SAFETY

Development and evaluation of a computable phenotype to identify pediatric patients with leukemia and lymphoma treated with chemotherapy using electronic health record data

(2019) Charles A. Phillips et al.   PEDIATRIC BLOOD & CANCER

Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records

(2019) Guergana K Savova et al.   CANCER RESEARCH

PheValuator: Development and evaluation of a phenotype algorithm evaluator

(2019) Joel N. Swerdel et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

(2019) Na Hong et al.   JOURNAL OF BIOMEDICAL INFORMATICS

High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP)

(2019) Yichi Zhang et al.   Nature Protocols

Adapting electronic health records-derived phenotypes to claims data: Lessons learned in using limited clinical data for phenotyping

(2019) Anna Ostropolets et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Natural Language Processing for EHR-Based Computational Phenotyping

(2018) Zexian Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse

(2018) Nicolas Garcelon et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Development of an automated phenotyping algorithm for hepatorenal syndrome

(2018) Jejo D. Koola et al.   JOURNAL OF BIOMEDICAL INFORMATICS

SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research*

(2018) Honghan Wu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records

(2018) Chia-Yen Chen et al.   Translational Psychiatry

Identifying heart failure using EMR-based algorithms

(2018) Geoffrey H. Tison et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

Evaluating automated approaches to anaphylaxis case classification using unstructured data from the FDA Sentinel System

(2018) Robert Ball et al.   PHARMACOEPIDEMIOLOGY AND DRUG SAFETY

A Bayesian latent class approach for EHR-based phenotyping

(2018) Rebecca A. Hubbard et al.   STATISTICS IN MEDICINE

Automated Feature Selection of Predictors in Electronic Medical Records Data

(2018) Jessica Gronsbell et al.   BIOMETRICS

Natural language processing and machine learning to identify alcohol misuse from the electronic health record in trauma patients: development and internal validation

(2018) Majid Afshar et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Automated and flexible identification of complex disease: building a model for systemic lupus erythematosus using noisy labeling

(2018) Sara G Murray et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The FDA Sentinel Initiative — An Evolving National Resource

(2018) Richard Platt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism

(2017) Jessica J Y Lee et al.   GENETICS IN MEDICINE

EHR-based phenotyping: Bulk learning and evaluation

(2017) Po-Hsiang Chiu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Enabling phenotypic big data with PheNorm

(2017) Sheng Yu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability

(2016) Jacqueline C Kirby et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Electronic medical record phenotyping using the anchor and learn framework

(2016) Yoni Halpern et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers

(2016) Cassandra Brady et al.   Applied Clinical Informatics

MIMIC-III, a freely accessible critical care database

(2016) Alistair E.W. Johnson et al.   Scientific Data

An integrated, ontology-driven approach to constructing observational databases for research

(2015) William Hsu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

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

(2015) Huan Mo et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources

(2015) Sheng Yu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts

(2015) Katherine P. Liao et al.   PLoS One

Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record

(2014) Chen Lin et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Launching PCORnet, a national patient-centered clinical research network

(2014) R. L. Fleurence et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

PCORnet: turning a dream into reality

(2014) F. S. Collins et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A quantifier-based fuzzy classification system for breast cancer patients

(2013) Daniele Soria et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Application of Information Retrieval Approaches to Case Classification in the Vaccine Adverse Event Reporting System

(2013) Taxiarchis Botsis et al.   DRUG SAFETY

Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts

(2013) Jesualdo Tomás Fernández-Breis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Electronic health records based phenotyping in next-generation clinical trials: a perspective from the NIH Health Care Systems Collaboratory: Table 1

(2013) Rachel L Richesson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

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

(2013) K. M. Newton et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A review of approaches to identifying patient phenotype cohorts using electronic health records

(2013) Chaitanya Shivade et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Computational Phenotype Discovery Using Unsupervised Feature Learning over Noisy, Sparse, and Irregular Clinical Data

(2013) Thomas A. Lasko et al.   PLoS One

Automating case definitions using literature-based reasoning

(2013) R. Ball et al.   Applied Clinical Informatics

Deep phenotyping for precision medicine

(2012) Peter N. Robinson   HUMAN MUTATION

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

(2011) Abel N Kho et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

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

(2010) Guergana K Savova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement

(2010) David Moher et al.   International Journal of Surgery

‘Deep phenotyping’: characterizing populations in the era of genomics and systems biology

(2009) Russell P Tracy   CURRENT OPINION IN LIPIDOLOGY