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Putting Semantic Web Ideas to Work

IO Informatics uses the Semantic Web to manage scientific data.

By John Russell

Sept. 5, 2008 | Turning Semantic Web technology into practical applications that enhance biomedical research was a driving force behind Robert Stanley’s and Erich Gombocz’s collaboration long before they founded IO Informatics. The explosion of data and the scientific literature convinced them that effective data management and data integration were critical for productive data analysis.

While many people recognized the same challenges and opportunities, Stanley and Gombocz were among the few who adopted semantic web ideas early and worked to incorporate them deeply into a scientific data management platform—Sentient Suite. Semantic software applications use the “RDF” (Resource Description Framework) data model to enhance life science researchers’ ability to understand how data fit together in complex biological systems (see, “Building a Google for Bioinformatics,” Bio-IT World, July 2007).

“We were looking ten years ago, right when RDF was starting to come out, at how we could solve these general problems and came up with our own semantic data model,” says Stanley. “We were thrilled when [Sir Tim] Berners-Lee and the rest of the [World Wide Web Consortium] started pushing this semantic data model because we knew we were right on target.”

It’s a decade since Stanley (CEO) and Gombocz (CSO) first met. Stanley was working on a business plan and interviewing potential CEOs. One candidate said, “I’d consider coming and working with you but you’ve got to let me bring Erich.” The two hit it off immediately. Jettisoning the would-be CEO, Stanley and Gombocz founded Biosentients in 2000 to hold the intellectual property (IP) they were developing. In 2003, the team offered the IP, business plan, and emerging software to the investment community, and Biosentients became IO Informatics. Stanley was elevated to CEO in April 2007.

Today, IO Informatics has a growing staff of 20 in North America and Europe, with roughly 30 customers and “hundreds of users”—not eye-popping numbers but indicative of strengthening market traction.

In broad terms, the Sentient Suite is comprised of five components: a Data Manager, a Process Manager, Web Query, Knowledge Explorer, and Image Interactor. The Sentient Data Manager module is the heart of the suite. It automates data loading and acts as a data repository. The Process Manager can be thought of as a widely generalizable LIMS system with workflow capability. IO Informatics’ patented intelligent multi-dimensional object technology powers both. “These basic features turn data from any source into web-accessible, searchable, annotatable, HIPAA-compliant items and allow end-users to pick data subsets and identify data networks from them,” says Stanley. The query and analytics tools are integrated with the Data Manager and Process Manager. Stanley has leveraged the company’s image-handling expertise as image analysis software sold to Berlex and Washington University, St. Louis.

“The Web Query and Knowledge Explorer then make this data easily and usefully available in various formats,” says Stanley. “Virtually any researcher or manager derives both knowledge and efficiency benefits by using the Web Query to search and browse data and dashboards derived from federated data and to export results to their own applications,” such as Partek or Spotfire. Informaticians can apply the Knowledge Explorer to visualize integrated networks and run semantic queries. This could help characterize a drug’s activities, stratify tumor types based on biomarkers, using SPARQL and advanced semantic query languages.


This article appeared in Bio-IT World Magazine.

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