Organizing Chaos

| September 12, 2014

A $10-million grant from NIH funds a much-needed craniofacial research database

An image of microCT scans of mouse embryo skulls. Data like this is stored in the FaceBase hub.


An image of microCT scans of mouse embryo skulls. Data like this is stored in the FaceBase hub. Photo courtesy of Yang Chai.

Data is essential to the work scientists and researchers do every day, but navigating the mountains of information available can be cumbersome at best, and dysfunctional at worst.

But with a five-year, $10 million grant from the National Institutes of Health, USC Viterbi Information Sciences Institute Fellow Carl Kesselman and his team are coming up with ways to make such data easy to upload, organize, navigate and, perhaps most importantly, collectively analyze as a scientific community.

The NIH grant will help fund the FaceBase Hub, a project aimed at advancing craniofacial research by better organizing datasets on development and deformities in the face and brain, in order for doctors, surgeons and researchers to more easily access and study the information. Kesselman’s team will organize a diverse set of projects from universities across the country that will provide data to the FaceBase website, FaceBase.org. Key members from other schools, including co-investigators Paul D. Thomas, an associate professor at the Keck School of Medicine of USC, and Yang Chai, associate dean of research at the USC Ostrow School of Dentistry, are contributing to the hub, which also includes teams from the University of Chicago and Harvard University.

FaceBase will be home to massive datasets for information including gene expression patterns, molecular and cellular interactions, and tissue morphology, as well as other aspects of how the face forms, with an easy-to-navigate labeling and organizing system that Kesselman likens to popular photo management software such as iPhoto.

“Scientists can spend up to half their time just trying to move their data around and figure out what they have and keep track of it,” said Kesselman, also a professor in the Daniel J. Epstein Department of Industrial and Systems Engineering. “We want to make searching for and organizing scientific data as easy as it is to get pictures off your smartphone to share, organize and access them.”

Scott Fraser, director of the USC Dornsife and Viterbi Translation Imaging Center, worked alongside Kesselman to secure the grant, seeing an opportunity to address a big problem. Fraser points out that masses of information and paperwork are a common problem.

“I have friends in the legal business and every once in a while they’ll archive huge boxes of file folders, and I wonder, Will anyone ever open those boxes again?” Fraser said. “Imagine that was scientific data, collected at great expense and effort. It would be a wasted opportunity not to know what is in the file box or how to interact with the contents. The last thing you want to do is go through it page by page to find what you want.”

Fraser’s lab builds powerful microscopes that can capture images of facial cell formation much deeper and faster than such instruments could even just a few years ago, which is hugely beneficial to craniofacial research but which poses other challenges.

“As imaging techniques have gotten better, we have this exploding ability to collect data,” Fraser said. “And our ability to analyze or interact with that data hasn’t kept pace.”

Until now. Using Kesselman’s FaceBase Hub, Fraser has a whole new infrastructure for working with the data he’s collected. And he finds collaborating with others that much easier and more straightforward.

“Those tools will impact so many researchers and allow us to better understand the data we’re collecting, and I think it will be generalized to other fields as well,” Fraser said.

The dental field in particular will see huge benefits. Chai, who is also the director of the Center for Craniofacial Molecular Biology at the Ostrow School, is a key collaborator on the FaceBase Hub and oversees one of its contributing projects. Chai’s team is a world leader in studying craniofacial development and examines birth defects like cleft palates, and has developed technology that will be incorporated into the hub.

The hub, Chai noted, “will not only impact what craniofacial researchers do, but will set us apart as a model for others to follow in research for the kidney and brain.”

By bringing together the engineering, dentistry, medical and Dornsife schools at USC (a collaboration Kesselman says “could only happen at USC”), all involved can tackle different aspects of problems in craniofacial research.

“My interest is in finding new and innovative ways that information technology and informatics can be used to advance science,” Kesselman said. “FaceBase is an example of a really wonderful application where we can work very closely with this research community on problems. And if solutions are found, they can radically improve people’s lives.”

And many are enthusiastic.

“It’s an amazing Viterbi success story,” Fraser said. “Carl is creating tools that are making a big impact in biology and biomedical work, and I think he’s going to take over the world.”

Published on September 12th, 2014

Last updated on August 5th, 2021

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