tranSMART Working Group

The tranSMART team is starting a monthly Working Group that meets monthly staring in January 2021.

The meeting will take place on the 4th Thursday at 11AM Eastern.  First date of the Working Group is 28 January 2021.

These meetings are intended to be open to discussion of any related tranSMART topic:  usage, data loading, analysis tools, bugs, questions, suggestions for new features, etc.

Please drop in to any session to ask a question, get some help, make a suggestions, or to just listen.

ZOOM:  https://us02web.zoom.us/j/81823361372

Isaac Kohane, MD Ph D

Isaac Kohane, MD Ph D

Professor & Chair of the Department of Biomedical Informatics at Harvard Medical School

Board Chairman of the i2b2 tranSMART Foundation

(more about Dr. Kohane)

The American Medical Information Association (AMIA) is honored to recognize Dr. Isaac Kohane with the Morris F. Collen Award for his substantial accomplishments to the field of biomedical informatics.  The Morris F. Collen Award is only awarded to the most distinguished informaticians.

Dr. Kohane is widely recognized as the lead investigator of a $25M National Center for Biomedical Computing (NCBC): Informatics for Integrating Biology to the Bedside (i2b2). i2b2 is an NIH-funded NCBC based at Partners HealthCare System in Boston. The key challenge that i2b2 is designed to address is that of creating a comprehensive software and methodological framework to enable clinical researchers to accelerate the translation of genomic and “traditional” clinical findings into novel diagnostics, prognostics, and therapeutics. i2b2 provides a technical solution to information exchange across institutions. It is now a standardized component of hundreds of analytic projects all over the world.

Next Community Meeting

Agenda
Informatics for Integrating Biology & the Bedside, or i2b2 is an NIH-funded enterprise clinical research platform, which contains a database model, application layer, and core APIs.

The i2b2 Software

tranSMART is a suite of data exploration, visualization, genomic analyses and ETL tools, which were developed by pharma for translational research studies.

The tranSMART Software

Common Data Model for i2b2 and tranSMART

COVID-19 4CE Consortium

Dr. Zak Kohane and several members of our Board of Directors have launched an urgent initiative with organizations around the world to rapidly collect aggregate data on hospitalized patients that are COVID-19 positive. The goal of this effort is to quickly collect data and publish the results.
Consortium for Clinical Characterization of Covid19 by EHR (4CE)

In this time of great need, the i2b2 tranSMART Foundation and the i2b2 community are working to combine national and international data for analyses of the COVID-19 affliction on our patients.

The 4CE Consortium is a globally distributed collaboration across health centers. In this first phase we are reaching out to other collaborators to join our 96 hospital collaboration who also have EHR data to share to augment the breadth and depth of the analyses we jointly work on.

Connect to 4CE

FALL 2020 European Virtual Symposium

Our FALL 2020 European Virtual Symposium was held on November 9, 2020.

The slide decks and recordings are available from the link below.

See the slide decks and recordings

Harvard Symposium Virtual Conference

The on-site Harvard Symposium was presented on June 11-12, 2020 as a Virtual Conference. The focus was on the COVID-19 virus. We had a great conference. If you missed it or are interested in reviewing the slide decks and recordings, visit the Symposium web pages. They are partially loaded and more coming …

Presentations and Videos
Virtual Poster Session
2020 Event Sponsors

COVID-19 Virtual Datathon-2020

The i2b2 tranSMART Foundation in partnership with Axiomedix and the Open Source Pharma Foundation (OSPF) are holding a Covid-19 Virtual Datathon-2020 on November 18-20, 2020.

The i2b2 tranSMART Foundation, with support from a grant from Dell Technologies, is creating a public instance of the latest version (v19.1) of the Foundation’s tranSMART software.  Hosted on AWS, tranSMART will be accessible freely with a link to an open-data collection of virus datasets, curated from GEO and other sources.  In addition, all of the additional almost 400 open tranSMART datasets may be loaded.

Data in the tranSMART Open Data Library, including data on a number of diseases areas including covid-19, may be loaded into the public tranSMART or downloaded to be used in another public or private version of tranSMART.

Visit the Virtual Datathon-2020 Webpages

About the i2b2 tranSMART Foundation

Overview

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History

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Community

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Management

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Board of Directors

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Working Groups

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COVID-19

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Sponsorships

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Get Involved

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Policies/Licensing

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What’s New

Check out our current activities and news!

Diane Keogh
Executive Director
Diane.Keogh@i2b2transmart.org

From The Executive Director’s Desk

COVID-19 Action!

In this time of great need, the i2b2 community is working to combine national and international analyses of the COVID-19 affliction on our patients.

There are two major initiatives that the Foundation is participating in at this time.

Grant to the Foundation from Dell Technologies

First, we are delighted to announce that Dell Technologies has given the Foundation a significant grant to expedite three projects that are focused on COVID-19 research working towards better understanding diagnosis, treatment and prevention of the disease. The three projects will be described in detail in upcoming Community Meetings. They are:

  • Public tranSMART v19 platform running on AWS with datasets that become publicly available. This project is in collaboration with Axiomedix.
  • With the explosion of articles and research labs studying the corona virus (over 6,000 articles from 25,000 authors), a special version of Profiles is being developed by Griffin Weber and will be available publicly.
  • i2b2 and tranSMART are being synchronized to the same data model so that direct data sharing will be possible between the Foundation platforms. We will have a few use cases and sample deployments available in the coming months.

4CE Consortium

Second, I want to tell you about the 4CE Consortium that was launched by Dr. Zak Kohane and several members of our Board of Directors. This urgent initiative with organizations around the world allowed labs with i2b2 to rapidly collect aggregate data on hospitalized patients that are COVID-19 positive. Their first publication is available as a preprint (click here) and will be published soon.

i2b2 ACT COVID ontology that has been developed

An initial ACT COVID ontology has been developed by the ACT Harmonization Committee. Note: Implementing this ontology is not necessary for this initial submission, but it might be helpful for you to look at the codes it uses as you try to identify your population of COVID-19 positive patients. click here for ACT COVID ontology

More information will be published here on our website as it becomes available. Be sure to join our Community Meetings and please attend the 2020 Harvard Virtual Symposium which will include focused sessions on these and other COVID-19 related projects.

Newsletters

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Press Releases

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Penn Medicine COVID-19 database uses i2b2 platform for it's robust ontology! Learn more here https://www.youtube.com/watch?v=aS51eqhVB60
#clinicalresearch #datasharing #COVID19 #clinicalresearch

i2b2 tranSMART January News Highlight : tranSMART Working Group starts January 28th, 11 AM EST. Join Us!
https://conta.cc/3t0beXW
#i2b2 #transmart #medicalinformatics #healthdata

i2b2 Platform used at University of Florida, Gainesville, to study Vitamin D deficiency and increased risk of COVID-19.
https://pubmed.ncbi.nlm.nih.gov/33418230/
#clinicalresearch #datasharing #COVID19 #clinicalinformatics

January 19th 11am EST
Next i2b2 tranSMART Community Meeting
Biomeris will discuss integration with REDCap and i2b2 as well as their client/server i2b2 extension called RCELL and Advanced Excel Exports. https://zoom.us/j/657679480
#clinicalinformatics #clinicalresearch #COVID19

COVID Authors is helping to connect researchers and collaborators of COVID-19 research. This international collaboration was made possible by 4CE International Consortium using the i2b2 platform.
https://hms.harvard.edu/news/searching-covid-19-publications
#clinicalresearch #datasharing #COVID19 #clinicalinformatics

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