Welcome to PhEMA Project Pages
This site contains information about the Phenotype Execution Modeling Architecture (PhEMA) project.
See more informaiton about the PhEMA project at the project wiki.
Software
PhEMA Project source code on GitHub
Publications/Presentations
| 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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