A Stanford University-led team is partnering with US defense contractor Northrop Grumman on a bioinformatics contract funded by the National Institute of Allergy and Infectious Diseases that will expand an immunology database and web portal.
Atul Butte, an associate professor of pediatrics and pathology at Stanford, will lead the team, which has members from the University of Buffalo and Technion-Israel Institute of Technology.
Stanford will partner with Northrop Grumman on a five-year, $30 million contract from the NIAID's Bioinformatics Integration Support Contract program. The partners will use the funds to continue gathering and housing data in the Immunology and Data Analysis Portal, or ImmPort — a repository for NIAID-funded experimental research into the human immune system. Stanford's share of the contract could be as much as $6 million.
ImmPort is part of a portfolio of bioinformatics projects that NIAID has contracted to Northrop Grumman, comprising a total of $47 million. The defense firm was awarded the ImmPort contract for NIAID's Division of Allergy, Immunology, and Transplantation in 2004 with help from the University of Texas Southwestern Medical Center, Kevric, Unicorn Solutions, and Biomind (BI 11/1/2004).
Northrop's Jeffrey Wiser, the program manager on the BISC contract, said that the partners spent the intervening years building up ImmPort and speaking with DIAT-funded researchers about the sorts of data that should go into the resource as well as how that data should be collected and curated before it is included in the repository.
In one project, researchers at UT Southwestern worked with scientists in the immunology community to develop standards for collecting data and then used these standards to develop templates for data submission and data capture, he told BioInform.
Last year, Northrop competed and won a second round of funding to continue working on ImmPort, beating out offers from a number of other undisclosed groups.
Stanford's Butte said that the main focus of the current collaboration will be on getting much more data from NIAID-funded research centers and trials into ImmPort and making it available to the scientific community.
They'll collect data from hundreds — possibly thousands — of clinical and vaccine trials and other studies including information from flow cytometry experiments, high-throughput sequencing, ELISA, and other kinds of molecular data, he told BioInform this week.
Besides data collection, Stanford's grant abstract explains that the team will work on methods for storing and exchanging data in ImmPort along with tools to integrate and retrieve information. They'll also develop capabilities for clinical data access, provide technical support, and "multiple workspace levels and analytic tools," the abstract states.
The team also plans to grow ImmPort's existing list of analysis tools. For example, they'll develop a program that can better interpret high-throughput data in the context of immunology, Butte said. They'll also build application programming interfaces that can link existing software to the database, he said.
Academia's contribution to the contract will include ontologies for immunology and infectious disease that will ensure that research results collected in ImmPort are expressed in a consistent fashion.
This part of the project will be handled by a team from the University of Buffalo that will be led by Barry Smith, a professor of philosophy, neurology, and computer science and director of UB's National Center for Ontological Research.
Smith and two colleagues will develop immunology-specific ontologies as well as computational tools and strategies that support data sharing and reuse through open ontology standards, according to UB. They'll also train NIAID-funded researchers to use the ontologies they provide for ImmPort, the university said.
Meanwhile, Shai Shen-Orr, an assistant professor at Israel's Technion Institute, said he'll work on providing "a global view" of current literature about various parts of the immune system; and also on developing tools to "interpret genomic-scale immunological signatures, in detailed cellular and immunological context."
He explained in an email to BioInform that the team will mine current immunology literature and combine information from it "with measured cell-specific data in a knowledgebase we have named ImmuneXpresso."
Here, the general idea is that "representing knowledge of the molecular biology of immune processes can enable the interpretation of complex immunological experimental results, and can enable search[es] across it," he explained.
"With ImmPort, our intention is to enable immunologists to input the results of their experiments into a web-based application and have immune concepts [such as] cells, cytokines [and so on] scored for the likelihood of their involvement," he said. This will allow users "to quickly interpret their omic data in a cell-type-specific fashion, as a set of interacting cells," he said.
Meanwhile, Northrop will continue in its management role, Wiser said. It'll also handle website development and will help curate the data before it's made available to the public, he said.
Northrop will also work with the Stanford team to figure out how to make the data they're collecting "useful" to the scientific community, he said.
Commenting on ImmPort's progress and the current development plans, Ashley Xia, the project officer for NIAID's BISC, said that she believes the project is moving in the "correct direction."
Xia oversees ImmPort's creation for NIAID. She told BioInform that the plans for this current phase of the project include encouraging more of the life science community to register to use and share the data provided through the platform.
Although anyone can use the system, ImmPort's developers only collect data from projects funded by NIAID, Xia said. This is to ensure that only good quality data makes its way into system, she explained.
When the data comes into ImmPort, it's curated and — in the case of clinical trial data — stripped of identifiers that could be used to trace it back to its donor, before being released for public use, she said.
Right now, there are about 11 curated datasets from six DIAT-funded projects stored in ImmPort including clinical trial and mechanistic research data. She said that there are other datasets in the pipeline that haven’t been released yet because they aren't complete.
A Home for Homeless Data
NIAID's ImmPort provides a much needed "home" for immunology data, which historically hasn’t had a place of its own, Stanford's Butte said.
NIAID funds a lot immunology-related molecular research and ImmPort provides a way to make this data available for "for downloading and secondary analysis," he told BioInform.
It could be used, for example, by consortia like the Cooperative Centers for Translational Research in Human Immunology and the Human Immunology Project Consortium, both of which are trying to figure out why some people don't respond to flu vaccines, he said.
They could use public information from ImmPort to analyze their data in the context of research results published by other institutions about their cohorts, he said.
It's also a useful resource for research into autoimmune diseases such as type 1 diabetes, lupus, scleroderma, and rheumatoid arthritis; organ transplantation; and infectious diseases, among other health conditions, he said.