Isotopes – elemental variations that contain different numbers of neutrons – can help researchers unearth the past of an object, especially the few hundred isotopes that are known to be stable over time. However, isotope analysis can be expensive and time-consuming and researchers have lacked a central data repository, meaning that most isotopic research has been conducted independently, with the resulting data stored in silos. Now, in a new article, the Texas Advanced Computing Center (TACC) has offered a deep dive into the creation of IsoBank, a community isotope database funded by the National Science Foundation (NSF).
“When people talk about the impact that technology has had on bioinformatics, they talk about genetic sequencing getting cheaper, but without the data becoming available through GenBank, the cost wouldn’t make much difference,” said Chris Jordan, manager for Data Management and Collections at the Texas Advanced Computing Center (TACC). “Unless you can compare your genome to all the other genomes that have been sequenced, you can’t make any sense of it. There is the potential here to do something similar with stable isotope data.”
The IsoBank project began in 2017, when an NSF-funded workshop led to a team of researchers publishing an opinion piece outlining the need for a centralized repository of isotopic data. Just a year later, the NSF made a bigger contribution: a $1.5 million, three-year grant to that same research team, a collaboration spanning TACC, the University of Wisconsin-Madison, the University of New Mexico and the University of Utah. The objective of the grant: to develop a globally accessible archive of isotopic data and analysis tools for that data.
IsoBank faces a number of challenges, chiefly storing the isotopic data and organizing the metadata that needs to accompany each piece of sample data in order to make it useful to the broader community. TACC, which was selected as a partner based on its experiencing handling massive record collections, is focused on appropriately representing and storing that metadata.
“We’re isotope experts, but we’re not experts in designing, building, and curating such a large database like this,” said Jonathan Pauli, associate professor of forestry and wildlife ecology at the University of Wisconsin-Madison. “TACC is really central in providing the expertise for us to be able to build IsoBank the way it should be.”
The team hopes that IsoBank will help researchers use multiple datasets – even those produced to answer “very different questions” – in a cohesive and cross-compatible way. Seth Newsome, an animal ecologist at the University of New Mexico, suggested using IsoBank to combine isotope datasets and examine how isotopes of various organisms express differently in different areas or time periods.
“There isn’t a field out there in natural science and medicine that’s not interested in isotopes,” Newsome said. “It’ll be cool to see this lead to collaborations of truly distant fields, like pharmacology and ecology, and biochemistry and archaeology.”
To read TACC’s Aaron Dubrow’s article on IsoBank, click here.