Graduate student Mark Bolding is heavily engaged in vision research. Specifically, he’s working on a diagnostic tool for schizophrenia based on eye movements. As does any researcher, he wants a safe place to store his data and share it with other investigators.
|Liz Lorbeer, Mark Bolding and John-Paul Robinson are conducting a pilot study to create an institutional repository using open-source software to collect, share and preserve the intellectual properties of the School of Optometry.|
Bolding was surprised when he began searching for one central repository on campus where he could do just that.
“There was nothing available,” Bolding says. “Data is one of our more valuable resources here. It is our currency.”
Bolding and Liz Lorbeer, associate director for content management at Lister Hill Library, decided to construct a vault for this information and recently were awarded a $5,000 grant to do so. The Express Library Digitization Award from the Southeastern/Atlantic Region of the National Network of Libraries of Medicine is intended to enable libraries to digitize historical materials or a unique collection to increase its accessibility within and outside the institution.
The two have enlisted the expertise of John-Paul Robinson, an architect for UAB IT Research Computing, to create an institutional repository using open-source software to collect, share and preserve the intellectual properties of the School of Optometry.
The idea is to seamlessly connect the school’s data, knowledge and scholarship to the greater global health and vision community by providing online access to images, data sets, streaming media, protocols, lab notes, article preprints, works in progress and brain-mapping data. By distributing unique data resulting from scientific pursuits, sharing that intellectual knowledge and making it accessible to the global health community, it would make materials created at UAB immediately accessible on the Internet to students, researchers and consumers.
“If this were money instead of data, we wouldn’t be stuffing it under our mattresses and keeping it in the labs,” Bolding says. “There would be a vault on campus where you could take it, and it would be managed.”
Initially the repository will focus on openly sharing digital assets created by the faculty and students of the School of Optometry and its Center for the Development of Functional Imaging. UAB’s School of Optometry was selected as an inaugural partner because of the broad range of disciplines that contribute to Vision Science, including visual psychophysics, neuroscience, computational vision and cognitive psychology.
While some ophthalmology departments have similar repositories for in-house users, few schools of optometry have such repositories, and there is little involvement from the optometry and vision-science community in university repositories. Lister Hill Library is a long-time member and supporter of the Association of Vision Science Librarians (AVSL), whose mission is to develop mechanisms for improving access to vision information. A repository of optometric materials would be a unique resource for the vision-health community.
NIH, NSF push availability
A database also would satisfy ongoing requirements by the National Institutes of Health (NIH) and the National Science Foundation (NSF) that research materials be made available publicly.
“The NIH has been a little more hard-nosed about it recently, and the NSF has said it’s going to make sure grants have this kind of statement or be considered incomplete,” Robinson says. “They’re saying you need to be thinking about this and ensure there is an institutional perspective.”
Lorbeer says some journal publishers no longer are accepting supplemental data — primarily because they don’t know how to subject it to peer review.
“If you send them the bench notes with your published paper, the reviewers don’t know how to handle that information,” Lorbeer says. “They can’t tell how accurate it is. It’s best left for an institutional repository open to the world for the scientific community to recreate the results.
“Journals are linking to a repository with those data sets and bench notes, so you can make the experimental data open,” Lorbeer says.
It’s not impossible for researchers to get their hands on information they want, but the NIH and NSF intend to lower the barrier to those transactions by encouraging the creation of repositories.
“It’s not that you wouldn’t want to give someone a phone call, but often you want to be satisfied immediately and reach the broadest audience,” Robinson says. “If you have to answer every phone call and request from every junior researcher that might be interested in the results you published in a very popular paper, you’re going to become a clearinghouse rather than a researcher.”
Focus on research
Most researchers create their own platforms to store their data or enlist a graduate assistant to do it. But this attempt to become experts on hosting infrastructure turns focus away from research.
For the UAB pilot, Research Computing is building platforms that campus researchers can leverage to build their equipment portfolio and computational capabilities for high-end performance computing and a broad range of services.
They are hosting a computer and running experiments with different pieces of software to try and determine the best way to expose digital collections to the outside world.
The model under development is the same most researchers use when they’re stepping through their own research protocols with their software, Robinson says.
“Researchers may not be interested in trying out a bunch of different pieces of software, but the platform needs are very similar,” Robinson says. “So far, everyone has had to do their own vertical implementation — top to bottom — independently. We can cut across that and just say ‘build on top of this common framework.’”
“We want to build something that people like to use, find pretty easy to use and want to share using the tool that’s created,” Lorbeer adds. “When you do research and you have your dataset, there’s pride in it. You’re not going to give it to just anybody. You want to make sure it’s in a secured place, and that it’s presented the way you as the scientist want to present it.”
Finding a way to protect and share research data is an issue every major research university is working on right now, Lorbeer says.
UAB’s team has spoken with the University of Minnesota, Purdue University and the University of California at San Diego among others to assess their experiences.
“They’re all struggling with the same issue we’re struggling with — to find the vehicle to load all of this information and be able to present it in a logical, easy and accessible way,” Lorbeer says. “You can load all of this data up, and it won’t mean anything if it’s not presented correctly.”
The design phase of the pilot grant began this past July. The setup phase began in the fall, and the group is in the beta test phase. They hope to have some answers by the spring.
“I hope by the end of April we know what road we want to go down,” Lorbeer says. “Right now we have many to choose from.”