i2b2: Informatics for Integrating Biology & the Bedside - A National Center for Biomedical Computing
Collaborations Academic Users' Group

The i2b2 Academic Users' Group has been set up to serve as a forum for those academic health centers interested in implementing the i2b2 software suite and is designed to support awareness of related activity amongst participating institutions, stimulate collaborations on developing and/or modifying elements of the i2b2 suite to better suit local or broader needs, and to provide guidance to the i2b2 team on issues ranging from software licensing to management of version control to collaborations with industrial partners.  All members participate in a Google Listserv and are encouraged to attend workshops and yearly meetings. Current membership is over 300 individuals from 50+ international organizations (see installations page for membership by institution). Shawn Murphy and the dev team have also implemented an i2b2 Community Wiki  for interaction between the community and developers.  Features include summaries of discussion threads on the AUG listserv, a Developer's Forum and a roster of i2b2-Sponsored Projects (the i2b2 Web Client) and i2b2-Related Projects (GARLIC, Health Ontology Mapper, HOMERUN, Registries using i2b2, SHRINE, and SMArt). Please contact us if you are interested in joining.

UPCOMING MEETINGS:

i2b2 AUG-SHRINE Annual Meeting

Tuesday, June 21, 2016

Joseph P. Martin Conference Center

Harvard Medical Center

77 Avenue Louis Pasteur

Boston, MA  02115

 

Registration required (no cost):  https://www.eventbrite.com/e/i2b2-aug-shrine-2016-conference-tickets-24789521125

 

Lodging information below:

 

The Inn at Longwood Medical

342 Longwood Avenue, Boston, MA 02115

617-731-4700

Group code:HMS10620

Cut off date for group rate: May 20, 2016

 

Precision Medicine 2016: Patient Driven

Wednesday, June 22, 2016

Joseph P. Martin Conference Center

Harvard Medical Center

77 Avenue Louis Pasteur

Boston, MA 02115

Sponsored by PIC-SURE BD2K Center of Excellence at HMS and

  the Department of Biomedical Informatics at HMS.

Registration required:  https://www.eventbrite.com/e/precision-medicine-2016-rogue-therapeutics-registration-24186059154

 


 

PREVIOUS MEETINGS:

Combined 4th Annual i2b2 AUG and SHRINE Conference and NLP Workshop

July 9-11, 2014

Wednesday, July 9 NLP Workshop

1:00  Introduction (Savova)

1:10  Keynote Presentiom" State of the Art of Temporal Relation Extraction (Bethard) (slides)

2:10  Methods for temporal relation discovery in the clinical narrative (Miller)

2:40  Extrinsic evaluation of temporal relation discovery system (Pradhan)

3:15  Temporally sensitive phenotypes: the use case of drug-induced liver toxicity (Lin) (slides)

3:45  Visualization tool for temporal relations from the clinical narrative (Finan) (slides)

4:15  Modules for temporal relation discovery from the clinical narrative in Apache cTAKES (Chen)

Thursday, July 10 AUG/SHRINE Conference

9:00   Future Directions for i2b2 and SHRINE (Kohane) (slides)

11:00 PCORI/SCILHS Update (Mandl/Murphy) (slides)

1:00   Clinical Trials Applications Roadmap

          -   Anne Klibanski, MD

          -   Lee Nadler, MD

          -   Shawn Murphy, MD, PhD

3:00   Working with AUG Community to harden i2b2 v.1.7 Plugins (Murphy, Xiao Dong, UIC & Community)

4:00   SHRINE FAQ (MacFadden) (slides)

5:00   Adjourn

Friday, July 11

8:30   Breakfast

9:00  Ontology Approaches (Phillips, Murphy) (slides)

10:00 Incorporating New Data Sources into i2b2

         -  Environmental Data (Patel) (slides)

         -  Social Media (Brownstein) (please email for info)

 

3rd Annual AUG Conference and NLP Workshop

June 18-19, 2013

Tuesday, June 18, 2013

9:00    NLP Workshop

12:00  Networking Lunch & Registration

1:00    Welcome and Introduction (Kohane)

1:15    Genomics Cell (Murphy) slides

1:45    SMART Update (Wattanasin) slides

2:15    i2b2 Roadmap (Murphy) slides

3:15    Break and Posters

4:15    Planning for the Future (Kohane)

5:15    Dinner on your own

Wednesday, June 19, 2013

8:00    Breakfast

8:30    Presentations by Members on plug-ins, improvements, etc

12:00 Close (Lunch for those attending SHRINE Conference)

SHRINE Conference

Wednesday, June 19, 12:00-5

Thursday, June 20, 8:30-12

i2b2 Tutorial (in conjunction with CTSA KFC Meeting and AMIA Annual Symposium): Developing an i2b2 Cell and Client Plugin

Wednesday, November 7, 2012  6-9 pm

Northwestern University (location TBD), Chicago, Illinois

Led by: Mike Mendis

Video available here.

This workshop took a step by step approach to implementing i2b2 at your institution, what technologies are used and any third party software that is required, such as application or database servers.  It continues by writing a new analytic "cell" and leveraging advanced services such as natural language processing.  The new cell was a fully working i2b2 cell that can receive and respond to i2b2 calls.  Next, an i2b2 webclient plugin wasl developed that sends a message to the cell and displays the response.  The Tutorial concluded with a roadmap for the near term and longer term i2b2 developments.

Due to the complex nature of this tutorial, the participants were asked to download and install the tutorial Virtual Machine (VM, see below) prior to attending.  The VM will run on any Windows or Macintosh machine and will contain a complete and installed i2b2 server, i2b2 webclient, application server, database server and any developments needed.  A completed cell and plugin will also be included.

Prerequisites:  Participants were asked to download and install the source code of the "i2b2 Tutorial" that is available at https://www.i2b2.org/software/ctsa2012.html prior to the workshop.

 

NLP Workshop at the i2b2 AUG Annual Conference, July 24 8:00-12:00, Joseph B. Martin Conference Center, Rotunda (3rd Floor),77 Avenue Louis Pasteur, Boston, MA 02115.  Video available here; meeting agenda below:

Tuesday, July 24

8:00-8:30         Breakfast and networking

8:30-8:40         Introduction    Guergana Savova, PhD, BCH and HMS

Part I: Semantic Processing

8:40-9:30         Keynote Presentation: Temporal Relations, ISO TimeML and Timelines

                             James Pustejovsky, PhD, Brandeis University

9:30-9:55          Relation Extraction for the Discovery of Severity and Body Location Modifiers

                              Dmitriy Dligach, PhD, BCH and HMS

9:55-10:20       Coreference    Timothy Miller, PhD, BCH and HMS

10:20-10:30     BREAK

Part II: Applications of NLP

10:30-11:00       cTAKES Applications:  i2b2 Phenotyping, PharmacoGenomics Research

                            Network, electronic Medical Records and Genomics (eMERGE),

                            Strategic Health Advanced Research Projects:Area 4 (SHARPn), Multi-

                            source integrated Platform for Answering Clinical Questions (MiPACQ),

                            Temporal Histories of Your Medical Events (THYME).

                                Guergana Savova, PhD, BCH & HMS

11:00-11:30       "How To" Phenotyping with NLP within the i2b2 platform

                                 Katherine Liao, MD

11:30-11:45        Infrastructure: cTAKES as (1) an i2b2 NLP Cell, architecture and demo,

                              and (2) an Apache Software Foundation project.

                                 Pei Chen, BCH and HMS

11:45-12:00        Discussion

5econd Annual i2b2 Conference, July 24-25, 2012, Joseph B. Martin Conference Center, 77 Avenue Louis Pasteur, Boston, MA.  

Tuesday, July 24  - Day One Video available here.

12:00  Registration and Networking Lunch

1:00    Welcome (Kohane)

1:15    Workshop for Version 1.7 (Murphy and team)

              -  Temporal Query Implementation

              -  Identity Management Cell Integration

              -  Infrastructure - Jboss 7, Bamboo, JIRA

2:30    Concurrent Field Reports and Poster Session

              Field Reports:

              -   Report from 3rd i2b2-Workshop Germany  (Uli Sax, PhD, Erlangen)

              -    i2b2 Wizard (Sebastian Mate, University of Erlangen)

              -   Semantic ETL into i2b2 with Eureka (Andrew Post, MD, Emory University)

              -   RECap i2b2 (Jonathan Bickel, MD, Boston Children's Hospital)

              -  CAD/C32 Ontologies for Meaningful Use (Michael Buck, PhD, NYC Dept. Health)

             Posters:

              -  Adding Episode-based Grouping to i2b2. Jeremy Nix, Parth Divekar, Rajesh Ganta,

                 Keith Marsolo, PhD, Cincinnati Children's Hosptial Medical Center

              -  Using i2b2 with SQL Server Reporting Services and SQL Server Analysis Services.

                 Jason Tillman, Parth Divekar, Keith Marsolo, Cincinnati Children's Med Center

              -  Gaining Orders of Magnitufe of Performance in an i2b2 Implementation at BIDMC.

                 Griffin Weber, BIDMC.

              - The University of Kansas' HERON Takes Flight: FY2012 Enhancements Include 

                 Support for NCI Cancer Center Designation (tumor registry, biospecimens, 

                 death index, and R integration), UHC Hospital Quality Measures, Technical

                 Diagnoses, Enhanced Medication and REDCap Registry Integration.  Tamara

                 McMahon, Nathan Graham, Daniel Connelly, Brennan Connolly, John Keighley,

                 Mani Nair, Ghargav Adagaria, Arvinder Choudary, Lemuel R. Waitman.

                 Division of Medical Informatics, Dept. Biostats, University of Kansan Med. Ctr.

              -  Tools for Improving Clinical Research Project Management.  Remo Mueller, Michael

                  Rueschman, Susan Redline, Div. Sleep Medicine, Brigham and Women's Hospital.

              -  Merging Age with Constraints to Select Patients by Age Range.  Deb Batson and

                  Colleagues, Children's Hospital Colorado.

              -  Modifiers Gone Wild.  Devjani Chatterjee and Jack London, Kimmel Cancer Center

                 and Thomas Jefferson University.

              - UC-ReX Using SHRINE...from Query to Cohort Discovery.  Travis Nagler, University of

                 California, Davis, and Ray Pablo, University of California, Irvine.

              -  Development of an Inter-University Oral Health Research Database. Dat Pham,

                  University of Texas Houston Health Sciences Center.

              -  Clinical Trender: Tracking Clinical Variables of a User-defined Cohort in i2b2.

                  Brian Ostasiewiski and Yarong Ge, Wake Forest University Baptist Med. Ctr.

              -  Untitled, Recombinant Data Corp.

              -  Untitled, Riccardo Bellazzi, University of Pavia

Wednesday, July 25: i2b2 Enhancements; Day 2 Video available here.

9:00-9:30      i2b2-CT: Proposal of community bundle for clinical trials support (Murphy and team)

9:30-10:00    SMART i2b2 Patient-centered View (Murphy and team)

10:00-10:30  NCBO i2b2 Ontology Tools (Phillips)

10:30-11:00  BREAK

11:00-11:30  GARLIC (Wilson)

11:30-12:00  Community Wiki Development

 

October 12, 2011 i2b2 v1.6 Workshop (in conjunction with annual CTSA IT KFC Meeting, Bethesda)

 i2b2-SHRINE Support for Clinical Trials and Substitutable Medical Applications and Reusable Technologies (SMART) project (Murphy) slides

 i2b2 Software 1.6 (Mendis) slides

Overall video

June 29-30, 2011 SHRINE Invitational Conference

Visit the post-conference website for presentations, list of attendees and to access SHRINE open source software; videos to follow.

June 28, 2011: NLP Workshop

Recent efforts in clinical NLP: Clinical Text Analysis & Knowledge Extraction System (cTAKES), overview (Savova)

Recent efforts in clinical NLP: cTAKES, programming example (Zheng)

Recent efforts in clinical NLP: Uncertainty discovery through NLP (Clark, MITRE)

Recent efforts in using clinical NLP for document classification: Autmoatic Retrieval Console (ARC)(D'Avolio, Boston VA)

Application of Clinical NLP: Rheumatoid Arthritis, an i2b2 Driving Biology Project (Karlson)

June 28-29, First Annual i2b2 AUG Conference, Boston, MA

Overview of i2b2 Roadmap (Kohane)

Software Plans 2011-2014 (Murphy, Phillips, Mendis)

Proof of Principle Use Case: Rheumatoid Arthritis Pheno to Geno (Plenge)

Ontologies (Murphy and team)

SMART (Substitutable Medical Applications, reusable technologies)

March 7, 2011: AUG Mini-Meeting, in conjunction with AMIA TBI Meeting.  6:30-8:30, Cyril Magnin 1 Room, 55 Parc Hotel, San Francisco; v.1.6 Workshop and Networking Reception.  Will be Webexed.

October 13, 2010: AUG Fall Meeting, in conjunction with the CTSA IT KFC Meeting, Natcher Conference Center, NLM, Bethesda, MD.  Slides from that meeting are available as follows:

Technical Workshop for i2b2 Version 1.6 (Murphy, Mendis)

i2b2 Plans 2010-2014 (Kohane, Murphy) (note - scroll to midpoint of slides for this presentation)

Sample Acquisition within i2b2 (Bry/Wilson) 

Hot Topic 1: Ontologies (Moderated by Davera Gabriel)

                           Field Reports from:

                           - UC Davis (Gabriel) (Slides not available)

                           -  i2b2-NCBO Collaboration (Shah)

                           -  HOM Integration with NCBO BioPortal (Wynden)

Hot Topic 2:  Mega i2b2: Registries and Networks (Moderated by Keith Marsolo)

                           Field Reports from:

                          -  SHRINE Update (Doug MacFadden)

                          -  ImproveCareNow Registry  (Pediatric IBD)(Marsolo)

                          -  CARRANet  (Pediatric Rheumatology)(Natter)

Hot Topic 3:  Temporal Queries (Zak Kohane, Griffin Weber)

March 10, 2010 (6-8 pm):  AUG Spring Meeting; in conjunction with AMIA Summit on Translational Bioinformatics, Parc 55 Hotel, San Francisco.  Dr. Murphy presented a technical perspective on the v1.4 full release (view slides).

October 28, 2009: AUG Business Meeting (preceding the CTSA IT KFC Meeting, Bethesda, MD).  Slides from that meeting are available as follows:

i2b2 Software Updates/Coming Attractions (Shawn Murphy)

Updates on i2b2 Federated Networks (SHRINE: Andrew McMurry)

Updates on Federated Networks (CICTR: Nick Anderson)

Managing Clinical Data for Research Using Epic and I2b2: A Case Study from Cincinnati Children's Hospital (Keith Marsolo)

Biosample Acquisition Software Update (Crimson:Lynn Bry)

Biosample Acquisition Software Update (Emerson/Housman)

Leveraging an i2b2 Implementation for Quality Improvement (U.Mass: Ralph Zottola and Ed Westrick)

A State-wide Application Using i2b2: Health Sciences So. Carolina (Iain Anderson and Jihad Obeid)

October 28, 2009:  AUG Code Workshop (as above) - active workshop, no slides.

May 5, 2009: AUG Business Meeting (in conjunction with UW CTSA Symposium and CICTR i2b2 Bootcamp) and Workshop.  Slides from that meeting are available at:

Preview of i2b2 Projects (Shawn Murphy)

Bug Tracking Jira (Mike Mendis)

ID Management (Shawn Murphy)

Web Client Plug Ins (Griffin Weber)

SHRINE Presentation (Andy McMurry)

October 15, 2008:  AUG Business Meeting (preceding the CTSA IT All Hands Meeting, Washington, DC).  Slides from that meeting are available as follows:

Update on Clinical Research Chart (Shawn Murphy)

Update on Federated Query Pilot (Weber)

Field Report from U. Mass. Medical School (Zottola)

Field Report from UCSF (Wynden)

Field Report from Cincinnati Childrens (Marsolo)

April 10, 2008:  AUG Business Meeting and Workshop (in conjunction with i2b2 Symposium: Instrumenting the Healthcare Enterprise for Discovery) Boston, MA). Slides available here.

CTSC CROSSOVER ACTIVITIES:

1.  Federated Query Pilots

Local: 

  • As the i2b2 team is heavily engaged in local CTSA  (Harvard Catalyst) IT activities, much of what we are doing to enable the Harvard teaching hospitals to share clinical data from their respective i2b2 instances has potential for CTSA colleagues interested in exploring the ability to federate across ever expanding networks.  The Catalyst/i2b2 IT team successfully launched beta testing of a Shared Health Research Information Network (SHRINE) on October 1, 2009 that links the i2b2 instances at Partners Healthcare (Massachusetts General and Brigham and Women's Hospitals), Childrens' Hospital Boston, and the Beth Israel Deaconness Medical Center.  This first iteration of SHRINE will return aggregate data counts for diagnoses, demographics, medications and selected lab values and will move next to sharing of Limited Data Sets.  This software will be freely available shortly.
  • Business Rules and Terms of Access developed to guide the Harvard Catalyst institutions regarding eligibility, access to data, and security are available to the community upon request to i2b2 .

National: 

  • The Cross-Institutional Clinical Translational Research (CICTR) project, led by Nick Anderson at U Wash and including colleagues at UCSF and UCDavis, successfully collaborated with Andy McMurry from the Catalyst/i2b2 team and Recombinant Data Corporation for a proof of principle federated query pilot using the prototype SHRINE architecture to share data across U Wash, UCSF, UCDavis and Harvard Catalyst.  CICTR successfully exchanged aggregate data on its network.
  • A supplement to the Harvard CTSA ("Catalyst") has enabled a national pilot project that is currently (2012) linking eight sites (Cincinnati Children's Hospital, University of Michigan, University of Washington, Wake Forest University Baptist Medical Center, Boston Children's Hospital, Partners HealthCare (Mass General and Brigham and Women's Hospitals), University of Texas and University of California San Francisco for the sharing of obfuscated aggregate patient data counts in two pilot projects which will look at the co-morbidities for autism and diabetes across this diverse network.  Content experts at each of the participating sites are driving the science questions and are supported by technical teams at each of the organizations and at Catalyst who have brought their i2b2 instances on line for this six month demo.  Data will be restricted to diagnoses and demographics for patients seen between 2009 and 2011.
  • The University of California is establishing a UCRex network that will link i2b2 instances at Irvine, Davis, San Francisco, Los Angeles and San Diego.

 

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