Get Smart

Knowledge Management
Winner: Centocor R&D nominated by Recombinant Data Corp.
Project: tranSMART

July 29, 2010 | One of the most gratifying aspects of awarding a Best Practices Award to a major pharmaceutical operation is to see that technology or platform find applications beyond the walls of the pharma itself. That certainly seems to be the case with tranSMART, the research data management project that was implemented at the Johnson & Johnson (J&J) subsidiary Centocor R&D, with help from Recombinant Data Corporation in Boston.

As Bio•IT World reported earlier this year (see, “Running tranSMART for the Drug Development Marathon,” Bio•IT World, Jan 2010), tranSMART provides a federated connectivity architecture that allows Centocor researchers to query the company’s wealth of drug data using a single tool. The tranSMART architecture minimizes the complexity and resources required to aggregate disparate research data, improving the productivity of the company’s researchers.

Leading the charge for Centocor was Eric Perakslis who, just days after accepting the Best Practices Award, took up a new role as J&J’s vice president of Pharma R&D IT (a position formerly held by John Reynders, who has taken a different role at J&J). Indeed, Perakslis says “a lot of the innovation we tried to do [with tranSMART] were things that made them seek me out for this job.”

The impetus behind tranSMART was the notion that modern drug development is expensive, tedious, and very data intensive. tranSMART has a search engine that indexes many sources of internal and external data, as well as links for further analysis by applications such as Ariadne Genomics Pathway Studio. Some text sources are hand-curated, such that the hits from these curated sources can be exported in semantic triples and visualized in network diagrams.

A Dataset Explorer allows users to easily query clinical trial data and focus on scientific questions rather than data processing, generating queries by phenotypes, genotypes, or a combination thereof. End users can view summary statistics about their queries, analyze gene expression or proteomic data through a link to the Broad Institute’s Gene Pattern application or view SNP data using linkage disequilibrium plots.

Both the search engine and the Dataset Explorer leverage the same underlying data warehouse—the Recombinant Data Trust. tranSMART reduces the delay between a query across disparate source systems and a result from days or weeks to a matter of minutes. Within about 12 months, Perakslis and colleagues had tranSMART deployed, including a variety of open-source components to help other institutions leverage the knowledge base. That is already happening, says Perakslis.

One example is the European Union’s Innovative Medicines Initiative (IMI), designed to eliminate hurdles in drug development. IMI has funded U-BIOPRED, involving thousands of respiratory disease patients, looking for drug targets and repositioned molecules, involving multiple biopharmas, academic groups and regulators coming together. Perakslis says J&J was eager to get involved, and has granted tranSMART to the consortium. Another outreach effort is with St. Jude Children’s Research Hospital in Memphis, integrating tranSMART into the Cure for Kids and pediatric oncology database for 172 countries. “It’s great to see people taking it up,” says Perakslis, particularly as it is a “slightly disruptive innovation” for a big pharma. “It’s not just free software, but you can tailor your investment to make it viral and useful, rather than just buying licenses and getting it to work.”

Another pharma has approached Perakslis about using tranSMART as a large, public repository for cancer data. For J&J, “It’s good business,” says Perakslis. “If you want a friend, be a friend.” J&J isn’t looking for anything in return, but “If some of these foundations find a drug target or an interesting compound, and they care to show it to us first, it doesn’t bother us!”

This article also appeared in the July-August 2010 issue of Bio-IT World Magazine. Subscriptions are free for qualifying individuals. Apply today.

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