Integrating Environment Data with Clinical Research

Presentation Time: 08:00 AM - 08:18 AM

Abstract Keywords: Environmental Health and Climate Informatics, Geospatial (GIS) Data/Analysis, Data Sharing, Data transformation/ETL, Population Health
Working Group: Climate, Health and Informatics Working Group
Primary Track: Applications
Programmatic Theme: Clinical Research Informatics

This demonstration presents software resources being developed to support scientists conducting research into the impacts of geospatial-based environmental factors on health, based on work being done under the NIEHS Connecting Health Outcomes Research and Data Systems (CHORDS) program. The demonstration will focus on tools aimed at assisting researchers in finding and integrating environmental data into clinical data sets.

Speaker:
Charles Schmitt, PhD
National Institute of Environmental Health Sciences

Authors:
Adam Burkholder, MS - NIEHS; Trisha Castranio, PhD - NIEHS; Lara Clark, PhD - NIEHS; Mike Conway, MS - NIEHS; David Fargo, PhD - NIEHS; Rupali Gupta, PhD - ASRC Federal; Marcus Jackson, MS - ASRC Federal; Mariana Kassien, PhD - NIEHS; Ann Liu, PhD, MPH - NIEHS; Mitchell Manware, MPH - NIEHS; Kyle Messier, PhD - NIEHS; Aubrey Miller, MD - NIEHS; Deep Patel, MS - NIEHS; Alison Motsinger-Reif, PhD - NIEHS; David Reif, PhD - NIEHS; Maria Shatz, PhD, MS - NIEHS; Umit Tokac, PhD - University of Missouri-St. Louis;

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The CALHN Critical Care Informatics System

Presentation Time: 08:18 AM - 08:36 AM

Abstract Keywords: Critical Care, Usability, Information Retrieval, Data Modernization, Clinical Decision Support
Primary Track: Applications
Programmatic Theme: Clinical Research Informatics

We developed the Central Adelaide Local Health Network (CALHN) Critical Care Informatics System (CCCIS) to enable clinical and operational staff easy access to relevant information extracted from the Electronic Medical Record. CCCIS represents the first step in a multistep program of work to establish South Australia as the leading health informatics network in Australia.

Speaker:
James Malycha, MBBS FCICM PhD
Central Adelaide Local Health Network

Authors:
Lukah Dykes, BSc - HeartAI; Adam Phillips, BSc BPharm (Hons) CHIA - HeartAI; Paul Lambert, BAppSc (Physio) MA (Int Health) - HeartAI;

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The Monarch Knowledge Graph and R Package

Presentation Time: 08:36 AM - 08:54 AM

Abstract Keywords: Knowledge Representation and Information Modeling, Omics (genomics, metabolomics, proteomics, transcriptomics, etc.) and Integrative Analyses, Controlled Terminologies, Ontologies, and Vocabularies, Information Visualization
Primary Track: Applications
Programmatic Theme: Translational Bioinformatics

Integrating genetic, phenotypic, and other data at scale is vital for disease diagnosis and mechanistic discovery. The Monarch Initiative addresses this by harmonizing global biomedical data into ontologies and knowledge graphs. We’ll review the Monarch knowledge graph and demonstrate the ecosystem's newest tool, the monarchr R package, which leverages tidy principles to dynamically query, manipulate, and visualize knowledge graphs for rare disease and other translational research.

Speaker:
Shawn ONeil, Ph.D.
University of North Carolina at Chapel Hill

Authors:
Brian Schilder, PhD - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Kevin Schaper, BS - University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Corey Cox, MS - University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Sarah Gehrke, BS - University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Peter Robinson, PhD - The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Chris Mungall, PhD - Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Melissa Haendel, PhD - University of North Carolina at Chapel Hill;

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The Secure Health Informatics Research Environment (SHIRE): Analytics architecture supporting data science and compliance

Presentation Time: 08:54 AM - 09:12 AM

Abstract Keywords: Data Modernization, Governance, Informatics Implementation
Primary Track: Applications
Programmatic Theme: Clinical Research Informatics

UNC School of Medicine and UNC Health have developed a new analytical environment: the Secure Health Informatics Research Environment (SHIRE), using Microsoft Azure. SHIRE supports modern data science needs in several ways: (1) performance, for analyses that require significant compute; (2) auditing, to ensure users are adhering to policies; (3) security, to restrict users from exfiltrating data; and (4) file formatting, to provide very large files in optimal formats (e.g., Parquet) rather than unwieldy CSVs.

Speaker:
Emily Pfaff, PhD, MS
UNC Chapel Hill School of Medicine

Authors:
Matthew Dunlap, MSc - UNC Health; Anna Jojic, MLS; Paul Kovach; John Powers, PhD - University of North Carolina at Chapel Hill; Ram Rimal, MS - UNC Health; Kellie Walters, MPH - UNC-Chapel Hill;

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