2nd Semi-Annual i2b2 User Group Meeting

Make plans now to attend the 2nd semi-annual i2b2 User Group meeting, hosted by the CTSI. The meeting will take place on May 20th in the Helen Wood Hall Auditorium (1w304) from 2pm – 4pm.  All users and prospective users are invited to review new features and other improvements in i2b2.  In addition, you’ll have an opportunity to ask for and vote on future additions and changes.

But exactly what is i2b2?

i2b2 stands for “Informatics for Integrating Biology and the Bedside.” It is a system developed by Harvard University’s i2b2 Center, an NIH-funded center for biomedical computing, that integrates with eRecord to allow researchers to more easily navigate the (clunky and arcane) system.

Through i2b2, researchers can query a wide variety of information in the university’s eRecord database — as well as a handful of other local sources including data from Flowcast and HBOC — and get data within a matter of minutes.

Paul Allen, Ph.D.

Paul D. Allen, Ph.D.

“It’s really useful for answering proof of concept questions,” said Paul D. Allen, Ph.D., research assistant professor in the Department of Neurobiology and Anatomy. “When we’re working to set up resident research projects and we want to know, for example, whether there are enough newborn babies here to test for congenital CMV infection, you can go in and ask how many babies were born here in the last year, and it will spit out a number. It’s magic.”

At the CTSI, clinical research informaticist Adam Tatro, M.S., R.N., runs an i2b2 training session every month, where new users can learn the ropes.

Allen said the program has helped tremendously with study design. Recently, his group wanted to know if pediatric patients with the airway disorder laryngomalacia had more severe obstructive sleep apnea than other kids who had undergone sleep studies. Allen’s group searched for kids’ sleep studies, sorting for those with and without the disorder.

“After writing the program to read the sleep study note we answered the question in about 20 minutes – and the answer was no, these kids do just fine,” said Allen.

Additionally, the program is constantly being updated. Recently, it gained the ability to sort by prescribed medications.

“That was a really good update,” said Allen. “The caveat is we don’t know if people actually took the medications, but we can see what’s prescribed after certain treatments.”

Adam Tatro, M.S., R.N.

Adam Tatro, M.S., R.N.

Though many researchers use it to interface with eRecord, the program’s capabilities go beyond that. Christine Annis, senior health project coordinator in the Department of Neurology, is her department’s coordinator for national research studies that come through NeuroNEXT, a network for early phase neuroscience clinical trials, and uses i2b2 to pull data from Flowcast and HBOC.

By querying the various databases, Annis can respond to NeuroNEXT feasibility questionnaires in a short period of time. Site feasibility responses inform the Network as to whether there are sufficient number of specific types of patients available within the Network.

“We are asked how many people have been seen in the last year at the University of Rochester who will meet the proposals criteria, and how many of those seen we think could will enroll in the proposal if it were funded,” said Annis. “I primarily use i2b2 for those two questions.”

Annis has used i2b2 to track down data for 45 different NeuroNEXT proposals, totaling more than 1,000 different queries. By being able to run the queries on her own she does not have to ask other departments to take time out or their busy schedule to run a query on their patient databases.

“i2b2 has saved me so much time,” she said.

For more information on i2b2, contact Adam Tatro at Adam_Tatro@URMC.Rochester.edu.

Note: Thanks to Sean Dobbin, who posted the original version of this story on December 11, 2014.

Director’s Update — May 2015

Every month, the CTSI Stories Blog will post excerpts from ongoing conversations with the institute’s co-directors.

Below, Nana Bennett discusses how the CTSI has enhanced the role of its Strategic Leadership Group (SLG).NanaBennett

Tell us a little about the SLG’s role in the CTSI.

Historically, the SLG was composed of a handful of leaders from across the university. They were chosen because they were not closely involved in the CTSI, but represented leadership of relevant areas in the medical center, e.g., clinical, educational and research. The hope was that this diverse group of people, coming from a variety of backgrounds, would serve as advisers to the CTSI.

In the past, we had a less formal structure than we do now. Starting this year — and we’re emphasizing this, in particular, in the run up to the renewal — we’re presenting various aspects of the CTSI to the SLG formally, and asking them to provide feedback. In addition, we have added two new members representing the community.  This has further broadened the scope of input from the group.

What has been discussed so far?

Population health was the first area we discussed.  We discussed the meaning of population health to different constituencies and what our focus on population health could mean to the CTSI.  We talked about how, sometimes, investigators aren’t fully aware of the community engagement resources available at places like the Center for Community Health, and that it is important to consider how they’re going to engage subjects in all aspects of a study, not just during enrollment. And we talked about how the CTSI could potentially serve as a facilitator in moving research in a direction that’s based on the needs of a community. For example, two pressing problems locally are obesity and mental health, so focusing on those areas could be a good fit for the CTSI.  We discussed ways to move these research priorities forward in the medical center.

At the next meeting, we talked about our funding programs — our pilot and incubator programs. We’re expecting the renewal RFA is limit pilot funding somewhat, so we’re going to need to focus on aligning our funding with key elements of our mission and vision. We are still in the very early stages, but we discussed a few ways that we might be able to tweak those programs, such as requiring a transdisciplinary team, requiring population health alignment, and focusing on the removal of barriers to translational research.  In addition, we discussed alignment of the many pilot funding opportunities across the medical center so that investigators understand all the opportunities, and have the capacity to choose the best fit for their research.

Next, we’re going to talk about team science, and how we can better support collaboration.  It has been very helpful to have this diverse, experienced group all come together to discuss these topics.

What else has changed about the SLG?

We’ve also added two members of the Community Advisory Council – Ann Marie Cook from Lifespan and Elissa Orlando from WXXI – to the SLG. Previously, the Community Advisory Council was advising the Center for Community Health, but now that they have a presence on the SLG, providing advice to the whole CTSI.  They have a more direct voice in the decisions we make, and they keep us on track in responding to community needs.


Previous director’s updates:
April 2015 – Karl Kieburtz talks about how the leadership is preparing for the Clinical and Translational Science Award renewals.
March 2015 – Martin Zand introduces himself and discusses his interest in informatics and population-based research.
February 2015 – Nana Bennett discusses the CTSI’s Seminar Series on population health.

January 2015 – Harriet Kitzman reflects on her time as a CTSI co-director.
December 2014  – Karl Kieburtz offers his takeaways from the CTSI all-hands retreat.
November 2014 – Nana Bennett speaks to the expansion of the role of the CTSI’s Community Advisory Council.
October 2014 – Harriet Kitzman discusses the science of team science.
September 2014 – Karl Kieburtz talks about why the CTSI is beefing up its informatics team.
August 2014 – Nana Bennett discusses the new Population Health pillar.
July 2014 – Harriet Kitzman offers her takeaways from the Mini Summer Research Institute.
June 2014 – Karl Kieburtz gives an overview of the CTSI’s six pillars.