This site contains information about the Phenotype Execution Modeling Architecture (PhEMA) project.
See more informaiton about the PhEMA project at the project wiki.
PhEMA Project source code on GitHub
| Title | Type | Location |
|---|---|---|
| CQL4NLP: Development and Integration of FHIR NLP Extensions in Clinical Quality Language for EHR-driven Phenotyping | Publication | AMIA Informatic Summits, 2021 |
| Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets | Publication | 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 |
| 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 |
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