Big data moves towards action to improve scientific research, health

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The announcement last week that 70 medical, research and advocacy groups in 41 countries—including the National Institutes of Health—agreed to share genetic and clinical information made headlines across the country. But to many already working in the “big data” realm, the news is just a welcome addition to the momentum of global projects and alliances already in motion.

Global alliance in motion

DELSA, the Data-Enabled Life Sciences Alliance, is one example of an alliance in motion. Launched in 2011, DELSA brings together scientists from around the world who share a vision of sustainable and shared access to science and healthcare data, tools and knowledge. President and Co-founder Gene Kolker, PhD, chief data officer at Seattle Children’s Hospital, said the big data tools and databases can be equated to a social network, such as Twitter or Facebook. “But the data-enabled approaches will allow scientists to share remedies for diseases and will lead to a healthier overall population, as opposed to an update on what your friend decided to eat for lunch,” he said.

Kolker and a wide range of experts meet through DELSA on an annual basis. They also virtually share ideas and progress every two weeks. DELSA members hail from academia, including Stanford, University of California San Diego and the University of Chicago, and industry, including EMC, Intel and PerkinElmer. The team also has an international mix: Germany, Israel, China, Russia, India and Canada are represented in DELSA.

To date, they have sketched out an approach and timeline to change how research is conducted and shared among partners in cell biology, human organisms and ecological systems. DELSA has also created working groups around projects that range from outreach in the developing world to a social networking platform that supports effective use of resources through community building and matchmaking between scientists. Through the platform, scientists will be able to connect with collaborators that have specialized skills or unique data sets.

Thumbs up for a checklist

DELSA weighed in this week on Nature’s decision to implement a checklist for authors submitting life sciences articles. The group applauded the steps the journal took to ensure reproducibility and transparency in life-sciences articles. “By encouraging researchers to make their data and metadata available, and to clarify analysis methods, the checklist will help to prevent mistakes from being propagated and resources from being wasted on dead-end experiments,” the letter said. Kolker and 20 fellow scientists signed off on the letter.

The grassroots approach in DELSA is perhaps the group’s strongest suit. “DELSA attracts doers—researchers that want to make a difference in our global society and believe that the best way to do so is to add their unique strengths to a community for a stronger and more effective effort,” he said.

Mining for the gold in research

The Kolker lab at Seattle Children’s Research Institute has contributed to that effort by developing and expanding two freely available web-based proteomics resources that enable more effective, large-scale study of the structure and function of proteins. MOPED (Model Organism Protein Expression Database) and SPIRE (Systematic Protein Investigative Research Environment) can be used to explore self-generated and publicly available datasets. “We’ve analyzed data that is publicly available, and made more sense out of it,” said Kolker.

That approach has been referred to as the “goldmine” approach, in which scientists dig into a data set and improve it, retaining the “gold.” Professor Lennart Martens, Ghent University, Belgium told GenomeWeb in May 2013 that the approach had really taken off in 2012, citing Kolker and other big data experts’ projects around the world.

When the National Institutes of Health closed a data repository in April 2011 due to funding woes, Martens helped launch PRIDE, which involved the transfer of more than one million protein modifications from 28 species and more than 30 different labs. Martens said it took heroic efforts to move these data. Databases like PRIDE and MOPED have been launched, in part, to capture data from multiple resources.

“It’s not just about a rat race,” said Kolker. “These projects and DELSA are examples of scientists working together in a smarter and collaborative way, and designing the work appropriately, based on the complexity of the project.”

To arrange an interview with Dr. Kolker, contact the Seattle Children’s public relations team at 206-987-4500 or via [email protected].