Poster Table of Contents

Below are the Virtual Posters that were submitted to the i2b2 tranSMART Foundation’s Harvard 2020 Virtual Symposium.

We used the Foundation SLACK’s Poster-Session Channel to hold all of the Posters and to allow questions and comments between the Authors and the community.

The meeting took place using ZOOM Webinar on June 11-12, 2020. We will have the virtual posters available throughout this time and through SLACK anyone can ask questions of the authors and the authors can respond when they have time.

This interactive site will remain available on SLACK for at least 2 weeks after the Virtual Symposium concludes.

Link to the SLACK Poster-Session-Discussion Channel

Poster #1 – tranSMART Platform v19

Peter Rice, Rudy Potenzone, Keith Elliston, COVID-19 tranSMART Project

The i2b2 tranSMART Foundation, through the tranSMART PMC (Product Management Committee) has released v19 of the open-source tranSMART Platform.

Poster #2

Peter Rice, Keith Elliston, Rudy Potenzone, tranSMART Platform v19

tranSMART for Genomics Data and Analysis – Existing public datasets containing genomics data and analyses
are being loaded in to a public version of the tranSMART Platform by Axiomedix. Research groups around the
world will be invited to add their datasets. Analysis using this platform can begin immediately. Funded by Dell Technologies.

Poster #3 – COVID-19 Knowledgebase and Knowledge Graph

A COVID-19 Knoweldgebase and Knowledge Graph, R Blevins, MK Elliston, R Potenzone, KO Elliston, Ingentium, Inc.

Ingentium developed a new Information Commons and Knowledge Network to capture and organize the latest information on the Sars-CoV-2 and related coronaviruses. We take advantage of the Ingentium machine learning tools to curate a body of unstructured content to create an information commons. The information commons is used as a substrate for NLP and semantic predication to build a knowledge network.

Poster #4 – Terminology Maintenance for i2b2

W. Scott Campbell, Carol Geary, Brendan Cope,
Jay Pedersen, Jerrod Anzalone

University of Nebraska Medical Center

Terminology Maintenance for i2b2

PROBLEM: ONC terminologies are constantly adding new codes and deactivating existing codes.

Objectives: Keep i2b2 ontology build current with recent Standards Development Organization terminology releases.

Methodology: Use transitive closure tables and current terminology to build new i2b2 metadata using the following pipelines:

  1. Building the pipeline for timely delivery and maintenance of i2b2  SNOMED CT CONDITION ontology
  2. Building the pipeline for timely delivery and maintenance of i2b2 RXNORM/NDC MEDICATION ontology
  3. Building the pipeline for timely delivery and maintenance of i2b2 LOINC LABS ontology

Poster #5 – i2b2 & tranSMART Data Schema

Griffin Weber, MD, PhD; Jeff Klann, PhD; Mike Mendis; Peter Rice

i2b2 & tranSMART Data Schema

Standardizing the data schema between i2b2 and tranSMART will improve interoperability. Additionally by adopting a well documented common data model we can facilitate research approaches that allow users to move between i2b2 and tranSMART, making use of the unique features and plugins of each platform.

Poster #6 – Visualizing Healthcare System Dynamics (HSD) in Biomedical Big Data

Nick Benik; Katy Borner, PhD; Nick Brown; Daniel Halsey; Isaac Kohane, MD, PhD; Griffin Weber, MD, PhD

Visualizing Healthcare System Dynamics (HSD) in Biomedical Big Data

Biomedical Big Data, such as electronic health records (EHR) and administrative claims, are records of patients’ interactions with the healthcare system. For example, a patient always has a white blood cell (WBC) count, but it only appears in an EHR when the patient seeks medical care and a physician thinks the patient needs the test. We created data visualizations to show that these interactions leave a signal in observational clinical data that contains valuable information, which could benefit biomedical research, clinical care, and health care policy.

Poster #7 – Real-time queries of millions of patients using probabilistic sketches

William Yu, PhD; Nick Benik; Nick Brown; Ken Huling; James Norman; Griffin Weber, MD, PhD

Real-time queries of millions of patients using probabilistic sketches

Clinical Query 2 (CQ2) is i2b2 at Beth Israel Deaconess Medical Center (BIDMC).

Poster #8 – Controlling the Brain’s Emotional Switch: Biased Cholinergic Input and Prelimbic and Infralimbic Projector Cell Body Localization within the Basolateral Amygdala

John M. Amodeo, Nguyen Vu, Grace C. Jones, James W. Warren, Alexander J. McDonald, David D. Mott

Controlling the Brain’s Emotional Switch: Biased Cholinergic Input and Prelimbic and Infralimbic Projector Cell Body Localization within the Basolateral Amygdala

The basolateral amygdala (BLA), consisting of the basolateral (BL) and lateral (LA) nuclei, is an important emotional processing center in the brain, assigning salient stimuli with emotional value or valence. Within the BLA, spatially segregated and genetically distinct pyramidal neurons (PNs) have been identified based on their correspondence to distinct behavioral stimuli. Recent studies have suggested that PNs located in the anterior portion of the BLA (BLAa) respond to negative valence stimuli and are involved in aversive behaviors and memories. In contrast, PNs located in the posterior BLA (BLAp) respond to positive valence stimuli and control appetitive behavior and memory. PNs in these regions convey emotional information through their projection to a variety of target regions in the brain. For example, PNs projecting to prelimbic (PL) cortex are located predominantly in the BLAa and are involved in fear acquisition. In contrast, PNs projecting to infralimbic (IL) cortex are located throughout the BLA, but particularly in BLAp. These infralimbic projecting PNs contribute to fear extinction. The mechanism by which these distinct PNs are modulated and whether this modulation differs depending on the projection target remains unclear.

Poster #9 – i2b2 1.7.12a

Jeff Klann, PhD; Michael Mendis; Shawn Murphy, MD PhD

i2b2 1.7.12a

Informatics for Integrating Biology and the Bedside (i2b2) is a well-established open-source clinical data warehousing and analytics platform in use at over 200 locations worldwide. It was first released in November 2007 and is presently in its eighth major release, version 1.7.12. The core i2b2 software offers a flexible, ontology-based data model, an application programming interface for patient-centric data retrieval, and a web-based cohort finding tool. A diverse set of community contributions provide add-ons and plugins for a wide variety of import, export, and analytics applications. Originally funded by the National Institutes of Health, it is now maintained by the i2b2-tranSMART foundation, which continues to refine the core software according to users’ needs.

In December 2019, i2b2 1.7.12 was be released, with a variety of improvements ranging from improved usability in the cohort finding tool to refactoring on the server. 1.7.12a included critical bug fixes and was released in May 2020. We will release 1.7.13 at the end of 2020.

Poster #10 – Arvados and CWL: Developing A COVID-19 Public Sequence Resource

Pjotr Prins, Peter Amstutz, Tazro Ohta, Thomas Liener, Erik Garrison, Michael R. Crusoe, Rutger Vos, Michael Heuer, Adam M Novak, Alex Kanitz, Sarah Wait Zaranek, Alexander Wait Zaranek, Jerven Bolleman, Joep de Ligt, Bonface Munyoki, Andrea Guarracino, Danielle Welter

Arvados and CWL: Developing A COVID-19 Public Sequence Resource

We present an Arvados and CWL use case developing a COVID-19 public sequencing repository (COVID-19 PubSeq) as part of the COVID-19 Virtual Biohackathon 2020. Arvados and CWL allow for the rapid prototyping of this resource that rapidly analyzes and incorporates uploaded sequences into a public pangenome using scalable, reproducible workflows. Results are made publically available in standard formats along with structured,validated metadata.

Poster #11 – The OSPF Data Commons: A Translational Research Resource forNeglected Diseases

MK Elliston, PM Rice, MV Hosur, J Menon, J UC, KO Elliston, N Rath

The OSPF Data Commons: A Translational Research Resource for Neglected Diseases

The Open Source Pharma Foundation and Axiomedix are collaborating on the implementation of an open patient data commons for the collaborative development of new disease treatments using an open source methodology. This project is initially focused on Tuberculosis, Nipah Virus, and Chikungunya Virus, and takes advantage of open data repositories such as NIH’s Gene Expression Omnibus. Recent advances comprise the inclusion of translational data for Dengue and Zika virus studies.  The OSPF Data Commons will be an evolving resource for OSPF and the Open Source Pharma community to facilitate clinical and translational research for neglected diseases in the developing world. Implementing this platform in tranSMART enables researchers to engage in meaningful analysis of multi-dimensional and high-dimensional patient data to explore and generate hypotheses. Additional disease content will be added as OSPF develops its portfolio of drug discovery and development programs. This platform implemented using tranSMART 19.

Meet Our Team

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Lillie Reyes
Lillie ReyesCEO / Founder
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Travis Hale
Travis HaleTechnical Manager
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Ethel Jensen
Ethel JensenResearch Lead
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