Open-access data resource aims to bolster collaboration in infectious disease research

February 21, 2018 by Katherine Unger Baillie, University of Pennsylvania
An international team of researchers has launched the Clinical Epidemiology Database, an open-access online resource enabling investigators to maximize the utility and reach of their data and to make optimal use of information released by others. Credit: University of Pennsylvania

Population-based epidemiological studies provide new opportunities for innovation and collaboration among researchers addressing pressing global-health concerns. As with the vast quantities of information emerging in other fields, from economic modeling to weather surveillance to genomic medicine, the technical challenges of sharing and mining gigantic datasets can hamper such efforts. A single epidemiological study—tracking the acquisition of functional resistance to malaria, or the relationship of diarrheal disease to developmental outcomes—may involve tens of thousands of clinical observations on thousands of participants from multiple countries.

To overcome these hurdles, an international team of researchers has launched the Clinical Epidemiology Database, an open-access online resource enabling investigators to maximize the utility and reach of their data and to make optimal use of information released by others.

The development of ClinEpiDB has been led by the University of Pennsylvania's David Roos, the E. Otis Kendall Professor of Biology in the School of Arts and Sciences, and Christian Stoeckert, research professor of genetics in Penn's Perelman School of Medicine, along with Jessica Kissinger, distinguished research professor of genetics at the University of Georgia's Institute of Bioinformatics, and Christiane Hertz-Fowler, professor at the University of Liverpool's Institute of Integrative Biology.

ClinEpiDB uses computational infrastructure established during the past 20 years for the Eukaryotic Pathogen Database, one of four national Bioinformatics Resource Centers for Infectious Disease supported by the U.S. National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, with additional support from The Wellcome Trust (UK) and others. EuPathDB is a thriving genomics resource for integrative analysis of microbial eukaryotes, such as the parasites that cause malaria, sleeping sickness, and other diseases. EuPathDB is currently accessed by more than 70,000 unique visitors monthly, from 100-plus countries around the world, and has been cited more than 13,000 times in the scientific literature to date.

"It is increasingly possible to generate spectacularly valuable, large-scale datasets, but how to store and manage this information so that people can make sensible use of it is arguably the overriding challenge of our day," says Roos. "The EuPathDB project has demonstrably helped translate the promise of infectious-disease genomics into practice, and with ClinEpiDB we are providing a resource to help get the information from large patient studies into the hands of those who can do the most good with it, while also protecting the confidentiality of ."

Bioinformaticist Brian Brunk oversees the EuPathDB as senior project manager, and molecular epidemiologist Brianna Lindsay is responsible for coordinating the ClinEpiDB initiative.

Many journals and funders encourage, and often require, scientists to make their study data available, but doing so in a useful way can be difficult for data-providers and users alike. ClinEpiDB aims to mitigate these issues by creating standardized processes for accessing and exploring complex clinical data. This new web resource introduces an intuitive interface, enabling users to explore data using point-and-click filtering, simple queries and more complex "search strategies" and a suite of exploratory statistical-analysis tools. The site also provides documentation of study design and background, contact information for data contributors, and links to study-related publications and resources.

According to Stoeckert, "establishing formal definitions of and relationships between data variables is one key to the success of this initiative. EuPathDB uses an OBO Foundry based ontology, aiding integration across datasets and establishing common, user-friendly terms for study details."

The ClinEpiDB launch presents as its inaugural study data from the Program for Resistance, Immunology, Surveillance and Modeling of Malaria project, or PRISM, led by Grant Dorsey, professor of medicine at the University of California, San Francisco, and Moses Kamya, professor and dean, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda. PRISM includes data from more than 40,000 clinical observations of 1,400 study participants, as one of several NIAID-funded International Centers of Excellence for Malaria Research

"The goal of PRISM project is to improve our understanding of malaria, and measure the impact of population-level control interventions," Dorsey notes. "This study represents seven years of work to date, from scores of researchers, with contributions from many hundreds of Ugandan kids at risk for malaria, as well as their families. It is exciting that ClinEpiDB makes it easy for anyone to browse and analyze the data and to quickly test parameters that may be associated with increased or decreased risk of serious malaria."

Further studies in the pipeline for release on the ClinEpiDB platform include additional ICEMR projects, and two large global enteric disease datasets funded by the Bill & Melinda Gates Foundation: the Global Enteric Multicenter Study, or GEMS, and the MAL-ED study on etiology, risk factors and interactions of enteric infections and malnutrition, and the consequences for child health and development.

Steve Kern, deputy director for quantitative sciences at the Gates Foundation says: "Our mission is to improve global health and reduce inequality, and achieving these goals depends on accessing and interrogating the wealth of available information produced by the global scientific community. We are optimistic that resources like ClinEpiDB will help make information produced by the foundation and its global partners available to all and enable us to take advantage of information from others, expediting scientific discovery and evidence-driven translation to improve human health worldwide."

Explore further: Multidrug-resistant malaria spread under the radar for years in Cambodia

Related Stories

Multidrug-resistant malaria spread under the radar for years in Cambodia

February 2, 2018
The most comprehensive genetic study of malaria parasites in Southeast Asia has shown that resistance to antimalarial drugs was under-reported for years in Cambodia. Researchers from the Wellcome Sanger Institute and their ...

Global maps created to show malaria hotspots

December 4, 2006
Global maps are being created that will define, for the first time in over 40 years, the distribution of malaria risk worldwide. The atlas will help those involved in malaria control.

Inequalities in malaria research funding in sub-Saharan Africa

June 28, 2017
A quarter of countries in sub-Saharan Africa receive very little funding for research into malaria despite having high malaria-related death rates.

Africa-led research to tackle the challenge of infectious diseases

October 24, 2017
Millions of people could benefit from a new study that is seeking novel solutions to the problems of infectious diseases and emerging epidemics in Africa.

New global migration mapping to help fight against infectious diseases

August 22, 2016
Geographers at the University of Southampton have completed a large scale data and mapping project to track the flow of internal human migration in low and middle income countries.

NIH launches first phase of microbiome cloud project

September 26, 2013
The National Institutes of Health (NIH) has launched the first phase of the Microbiome Cloud Project (MCP), a collaboration with Amazon Web Services that aims to improve access to and analysis of data from the Human Microbiome ...

Recommended for you

Researchers seek vaccine for 'traveler's diarrhea'

September 25, 2018
Every year, millions of people have vacations and business trips ruined when they succumb to "traveler's diarrhea" during their journeys. A major cause of traveler's diarrhea is bacteria called Enterotoxigenic E. coli, or ...

New way of determining treatment for staph infections cuts antibiotic use

September 25, 2018
Using a clinical checklist to identify eligible patients, doctors were able to shorten the antibiotic duration for patients with uncomplicated staphylococcal bloodstream infections by nearly two days, Duke Health researchers ...

Breakthrough in designing a better Salmonella vaccine

September 24, 2018
UC Davis researchers announce in the Proceedings of the National Academy of Sciences this week a breakthrough in understanding which cells afford optimal protection against Salmonella infection—a critical step in developing ...

Antifungal agent found to be possible treatment for porphyria

September 24, 2018
A large team of researchers from Spain, France and the U.S. has found that a common antifungal agent might be useful as a treatment for a rare type of porphyria. In their paper published in the journal Science Translational ...

New findings on the muscle disease Laing early-onset distal myopathy

September 24, 2018
New avenues are now being opened toward treatment of Laing distal myopathy, a rare disorder that causes atrophy of the muscles in the feet, hands and elsewhere. In a study published in the journal PNAS, researchers have identified ...

Insulin shows great potential against chronic colitis

September 24, 2018
Diabetes is not the only disease on which insulin has an effect, it appears. In a new study using tests on mice, researchers from the University of Copenhagen, among others, have discovered a new method for treating chronic ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.