tranSMART and i2b2 Show that Open Source Software Can Fuel Precision Medicine

Posted on April 19, 2017 I Written By

Andy Oram is an editor at O’Reilly Media, a highly respected book publisher and technology information provider. An employee of the company since 1992, Andy currently specializes in open source, software engineering, and health IT, but his editorial output has ranged from a legal guide covering intellectual property to a graphic novel about teenage hackers. His articles have appeared often on EMR & EHR and other blogs in the health IT space.

Andy also writes often for O’Reilly’s Radar site (http://oreilly.com/) and other publications on policy issues related to the Internet and on trends affecting technical innovation and its effects on society. Print publications where his work has appeared include The Economist, Communications of the ACM, Copyright World, the Journal of Information Technology & Politics, Vanguardia Dossier, and Internet Law and Business. Conferences where he has presented talks include O’Reilly’s Open Source Convention, FISL (Brazil), FOSDEM, and DebConf.

Medical reformers have said for years that the clinic and the research center have to start working closely together. The reformists’ ideal–rarely approached by any current institution–is for doctors to stream data about treatments and outcomes to the researchers, who in turn inject the insights that their analytics find back into the clinic to make a learning institution. But the clinicians and researchers have trouble getting on the same page culturally, and difficulties in data exchange exacerbate the problem.

On the data exchange front, software developers have long seen open source software as the solution. Proprietary companies are stingy in their willingness to connect. They parcel out gateways to other providers as expensive favors, and the formats often fail to mesh anyway (as we’ve always seen in electronic health records) because they are kept secret. In contrast, open source formats are out for everyone to peruse, and they tend to be simpler and more intuitive. As open source, the software can be enhanced by anyone with programming skill in order to work with other open source software.

Both of these principles are on display in the recent merger announced by two open source projects, the tranSMART Foundation and i2b2. As an organizational matter, this is perhaps a minor historical note–a long-awaited rectification of some organizational problems that have kept apart two groups of programmers who should always have been working together. But as a harbinger of progress in medicine, the announcement is very significant.

tranSMART logo

Here’s a bit about what these two projects do, to catch up readers who haven’t been following their achievements.

  • i2b2 allows doctors to transform clinical data into a common format suitable for research. The project started in 2004 in response to an NIH Roadmap initiative. It was the brainchild of medical researchers trying to overcome the frustrating barriers to extracting and sharing patient data from EHRs. The nugget from which i2b2 came was a project of the major Boston hospital consortium, Partners Healthcare. As described in another article, the project was housed at the Harvard Medical School and mostly funded by NIH.

  • The “trans” in tranSMART stands for translational research, the scientific effort that turns chemistry and biology into useful cures. It was a visionary impulse among several pharma companies that led them to create the tranSMART Foundation in 2013 from a Johnson & Johnson project, as I have documented elsewhere, and then to keep it open source and turn it into a model of successful collaboration. Their software helps researchers represent clinical and research data in ways that facilitate analytics and visualizations. In an inspired moment, the founders of the tranSMART project chose the i2b2 data format as the basis for their project. So the tranSMART and i2b2 foundations have always worked on joint projects and coordinated their progress, working also with the SMART open source API.

Why, then, have tranSMART and i2b2 remained separate organizations for the past three or four years? I talked recently with Keith Elliston, CEO of the tranSMART, who pointed to cultural differences as the factor that kept them apart. A physician culture drove i2b2, whereas a pharma and biochemistry research culture drove tranSMART. In addition, as development shops, they evolved in very different ways from the start.

tranSMART, as I said, adopted a robust open source strategy early on. They recognized the importance of developing a community, and the whole point of developing a foundation–just like other stalwarts of the free software community, such as the Apache Foundation, OpenStack Foundation, and Linux Foundation–was to provide a nurturing but neutral watering hole from which many different companies and contributors could draw what they need. Now the tranSMART code base benefits from 125 different individual contributors.

In contrast, i2b2 started and remained a small, closely-knit team. Although the software was under an open source license, the project operated in a more conservative model, although accepting external contributions.

Elliston says the two projects have been talking for the last two and a half years about improving integration and more recently merging, and that each has learned the best of what the other has to offer in order to meet in the middle. tranSMART is adopting some of i2b2’s planning, while i2b2 is learning how to organize a community around its work.

Together they believe their projects can improve more quickly. Ultimately, they’ll contribute to the movement to target cures to patients, proceeding now under the name Precision Medicine. Fund-raising and partnerships will be easier.

I have written repeatedly about these organizations to show the power that free and open source software brings to medicine. Their timely merger shows that open source overcomes cultural and institutional barriers. What it did for these two organizations it can do for the fractured landscape of hospitals, clinics, long-term care facilities, behavioral health centers, and other medical institutions struggling to work together. My hope is that the new foundation’s model for collaboration, as well as the results of its research, can slay the growing monster of health care costs and make us all healthier.