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This wiki contains information about the Phenotype Execution Modeling Architecture (PhEMA) project


Software

PhEMA Project source code on GitHub

PhEMA-Arch1.png

Publications/Presentations

Title Type Location
CQL4NLP: Development and Integration of FHIR NLP Extensions in Clinical Quality Language for EHR-driven Phenotyping Paper accepted AMIA Informatic Summits, 2021
Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets Paper accepted AMIA Informatic Summits, 2021
Identifying Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks Publication Journal of Biomedical Informatics, 2020
Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms Publication AMIA Annu Symp Proc. 2020 Mar 4;2019:755-764
PhEMA –The Phenotype Execution and Modeling Architecture Technical Demonstration Mobilizing Computable Biomedical Knowledge Annual Meeting, 2019
Subphenotyping Depression using Machine Learning and Electronic Health Records Publication Learning Health Systems, 2020
Data‐driven discovery of probable Alzheimer's disease and related dementia subphenotypes using electronic health records Publication Learning Health Systems, 2020
Toward cross‐platform electronic health record‐driven phenotyping using Clinical Quality Language Publication Learning Health Systems, 2020
Feasibility of Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language Podium Presentation AMIA 2020
Identification of Alzheimer's Disease Subtypes from Electronic Health Records Using a Data-Driven Approach Podium Presentation AMIA 2020
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries Publication Journal of Biomedical Informatics, 2019
Developing a portable natural language processing based phenotyping system Publication BMC medical informatics and decision making, 19, Article number: 78 (2019)
Identifying Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks Publication arXiv preprint arXiv:1904.04990
Predictive Modeling of the Risk of Acute Kidney Injury in Critical Care: A Systematic Investigation of The Class Imbalance Problem Publication AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:809-818
Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care Paper/Presentation MEDINFO 2019: the 17th World Congress of Medical and Health Informatics
Predictive Modeling of the Risk of Acute Kidney Injury in Critical Care: A Systematic Investigation of The Class Imbalance Problem Paper AMIA Summits on Translational Science Proceedings, 2019
Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms Paper AMIA 2019
Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study Paper AMIA 2019
Enhanced Execution of Standards-Based EHR Phenotype Algorithms. Poster AMIA Informatics Summit 2019
Manuscript A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and EHR environments. PhEMA representation of BPH case algorithm) Publication JAMIA
Portable Phenotyping System: A Portable Machine-Learning Approach to i2b2 Obesity Challenge Publication 2018 IEEE International Conference on Healthcare Informatics Workshop (ICHI-W)
Abstract An Evaluation of the Feasibility of Implementation of Computable Cancer Phenotyping With Pathology Records From Cerner Electronic Health Record System, (Poster) Poster Presentation College of American Pathologists 2017 The Pathologists' Meeting
The Phenotype Execution and Modeling Architecture (PhEMA) – A Standards-Based Composition of Software for Phenotype Algorithm Development (Abstract, Slides) Podium Presentation AMIA Joint Summit 2016
Porting a Natural Language Processing Algorithm to Extract Findings from Colonoscopy Pathology Reports. (Abstract, Slides) Podium Presentation AMIA Joint Summit 2016
Developing Executable Phenotype Algorithms Using the KNIME Analytics Platform. (Proposal, Slides) Tutorial Presentation AMIA Joint Summit 2016
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. (Paper, Slides, KNIME Workflows for this presentation) Paper Presentation AMIA Joint Summit 2016
Strategies for Cross-Institutional Collaborations of EHR-Driven Phenotyping Poster Life Science Tennessee 2015
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME Podium AMIA 2015
FUT2 polymorphism (rs492602) associates with vitamin B12 deficiency, but may be independent with proton pump inhibitor or metformin usages, diabetes mellitus, and thyroid diseases Poster ASHG 2015
Harmonization of Quality Data Model with HL7 FHIR to Support EHR driven Phenotype Authoring and Execution: A Pilot Study Poster AMIA 2015
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools Poster AMIA 2015
Desiderata for computable representations of electronic health records-driven phenotype algorithms Publication JAMIA - Sept 5, 2015
A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution Poster MedInfo 2015 - August 2015
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research Publication JAMIA - July 29, 2015
Implementing PheWAS in i2b2 Presentation i2b2 Conference - June 2015
Integration of i2b2 with the Phenotype Execution and Modeling Architecture (PhEMA) Presentation i2b2 Conference - June 2015
PhEMA: Phenotype Execution and Modeling Architecture Presentation Mayo Clinic / Dr. Shawn Murphy - May 2015
PhEMA: Phenotype Execution and Modeling Architecture Presentation S&I CQF - April 2015
Tutorial AMIA Joint Summit 2015
Porting a Natural Language Processing Algorithm to Extract Findings from Colonoscopy Pathology Reports. Podium Abstract AMIA Joint Summit 2015
A Semantic Framework for Quality Data Model to Support EHR-driven Phenotype Authoring And Execution Podium Abstract AMIA Joint Summit 2015
A Prototype for Executable and Portable Electronic Clinical Quality Measures Using the KNIME Analytics Platform Paper AMIA Joint Summit 2015
A Modular Architecture for Electronic Health Record-Driven Phenotyping Paper AMIA Joint Summit 2015
Evaluation of Existing Phenotype Authoring Tools for Clinical Research Poster AMIA 2014
Qualitative Evaluation of Three Phenotype Information Models to Find Methotrexate Liver Injury Abstract Presentation AMIA 2014