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This wiki contains information about the Phenotype Execution Modeling Architecture project

Outline of Proposed Study

Applications/Tools

PhEMA Authoring Tool - v0.5
PhEMA Data Element Repository REST Documentation
Data element repository SPARQL endpoint
VSMC wrapper over VSAC
PhEMA CTS2 editable Value Set service
KNIME Demonstrations

AMIA-TBI/CRI 2016

A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform (QDM-KNIME-i2b2)
Developing Executable Phenotype Algorithms using the KNIME Analytics Platform
Porting a Natural Language Processing Algorithm to Extract Findings from Colonoscopy Pathology Reports
The Phenotype Execution and Modeling Architecture (PhEMA) – A Standards-Based Composition of Software for Phenotype Algorithm Development

Publications/Presentations

Title Type Location
Qualitative Evaluation of Three Phenotype Information Models to Find Methotrexate Liver Injury Abstract Presentation AMIA 2014
Evaluation of Existing Phenotype Authoring Tools for Clinical Research Poster AMIA 2014
A Modular Architecture for Electronic Health Record-Driven Phenotyping Paper 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 Semantic Framework for Quality Data Model to Support EHR-driven Phenotype Authoring And Execution Podium Abstract AMIA Joint Summit 2015
Porting a Natural Language Processing Algorithm to Extract Findings from Colonoscopy Pathology Reports. Podium Abstract AMIA Joint Summit 2015
Tutorial AMIA Joint Summit 2015
PhEMA: Phenotype Execution and Modeling Architecture Presentation S&I CQF - April 2015
PhEMA: Phenotype Execution and Modeling Architecture Presentation Mayo Clinic / Dr. Shawn Murphy - May 2015
Integration of i2b2 with the Phenotype Execution and Modeling Architecture (PhEMA) Presentation i2b2 Conference - June 2015
Implementing PheWAS in i2b2 Presentation i2b2 Conference - June 2015
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research Publication JAMIA - July 29, 2015
A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution Poster MedInfo 2015 - August 2015
Desiderata for computable representations of electronic health records-driven phenotype algorithms Publication JAMIA - Sept 5, 2015
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools Poster AMIA 2015
Harmonization of Quality Data Model with HL7 FHIR to Support EHR driven Phenotype Authoring and Execution: A Pilot Study Poster 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
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME Podium AMIA 2015
Strategies for Cross-Institutional Collaborations of EHR-Driven Phenotyping Poster Life Science Tennessee 2015
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. (Paper, Slides) Paper Presentation AMIA Joint Summit 2016
Developing Executable Phenotype Algorithms Using the KNIME Analytics Platform. (Proposal, Slides) Tutorial 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
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