Although space science may seem a long way from biomedicine, and NASAs Jet Propulsion Laboratory (JPL) knows more about the surface of Venus than about the proteins on cell surfaces, JPL has made finding biologic samples for biomarker studies a lot easier, courtesy of software originally written to foster collaboration among planetary scientists.
The database collaboration is a product of the Informatics Working Group in the Early Detection and Research Network (EDRN), which is coordinated through the National Cancer Institutes Division of Cancer Prevention. EDRNs mission is to discover and validate cancer biomarkers and diagnostic tests for clinical application, said EDRN program director Sudhir Srivastava, Ph.D.
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Srivastava described the informatics effort as a kind of "yellow pages" for cancer researchers. "We have been funding tissue biorepositories over the years, but there was no way of finding out who had what," he said. "The goal was to have seamless access to all the resources."
The project was modeled on the Planetary Data System, a large software network that serves space science, a field notorious for its data glut. "Were used to working with scientists to help them share data they collect at their own institutions," said Daniel Crichton, a senior computer scientist at JPL. "We make it more usable through software technology."
JPL experts developed a layer of software for EDRN, just as they had for space scientists, that translates terminology used in local databases into standard jargon. "We wanted the data to remain in its native format so it would remain integrated with existing processes at home institutions," Crichton said. "We wanted the ability to make the links without them needing to redo their systems."
Registered users access the EDRN system by logging on through a password-protected home page and answering a series of questions. "You make your selections from a series of drop-down menus. Its pretty easy to do," said Melvyn Tockman, M.D., Ph.D. Tockman, a professor of oncology and medicine at the H. Lee Moffitt Cancer Center and Research Institute at the University of South Florida, Tampa, is both an adviser on the project and a user of the informatics system.
"You select the institution you want to query or the tissue type and let the engine do the searching for you," Tockman explained. "It works almost instantaneously. ... Its so easy that even an M.D. can figure it out."
The database contains details about each specimen. "It does not just say lung cancer, but whether its frozen or paraffin-embedded, when it was collected, and a little about the demography of the population from which it was collected," Tockman said. "This magnifies the utility of the specimens."
A critical element of the project was programming the software to translate from local databases into a structured language, called "common data elements." The software translates field names from, say, "sample ID number" to "sample number," allowing institutional databases to remain unchanged. In creating the translators, Tockman said, "JPL has been particularly insightful. They have developed an interface that runs each time a query is received, allowing us to use legacy databases that are already up and running. We do not need to rewrite our legacy programs, thank heavens."
Although the informatics project was initially intended as a smart catalog of samples housed at institutions that participate with EDRN, eventually it could also transfer digitized photos or even genetic data. Tockman plans to search for gene chips relevant to his research on biomarkers for lung cancer. "We anticipate having access to a catalog of microarrays," he said. "If we saw some that might be useful, wed request the arrays directly over the Web."
Before establishing the informatics network, the NCI had to assure institutional review boards that patients privacy would be protected. "The key challenge was getting IRB approval," said Srivastava. He added that the software strips out personal identifiers before any data leaves local institutions.
When the network formally began operating last September, it linked seven research institutions: Fred Hutchinson Cancer Research Center, Seattle; Creighton University, Omaha, Neb.; University of Michigan, Ann Arbor; University of Pittsburgh, Pa.; Moffitt Cancer Center and Research Institute; the University of Texas at San Antonio; and the University of Colorado. The University of Texas M. D. Anderson Cancer Center, Houston, and Brigham and Womens Hospital, Boston, are in the process of joining.
In science, Crichton pointed out, "The more data the better, the more data types the better. If you can increase the statistical power by interconnecting institutions, that certainly helps in the discovery process."
The point has not been lost on cancer researchers, Srivastava added. "Since our [November] presentation to the Board of Scientific Advisers, [people from] many programs in the NCI have contacted us. Were very happy about this technological platform, and we want to share it."
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