The goal of this research is to help researchers develop and use relatively simple tools to describe species in a way that make those descriptions easier to share with other scientists and easier for computers to process and analyze. The approach is bottom-up and iterative, involving the rapid prototyping of tools, combining of existing tools, and the tailoring of applications developed for one purpose but now being reused for this scientific activity. Innovation from this project is applicable to the long-term development of open source software initiatives serving labs throughout the world. The project provides rich, real-world training for graduate students in library and information sciences, training them to be much needed cross-disciplinary researchers in a field desperate for...
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National Science Foundation
National Science Foundation
Taxonomists are scientists who describe the world’s biodiversity. These descriptions of millions of species allow scientists to do many different kinds of research, including basic biology, environmental science, climate research, agriculture, and medicine. The problem is that describing any one species is not easy. The language used by taxonomists to describe their data is complex, and typically not easily understandable by computers nor even other scientists. This situation makes it harder to search for patterns across millions of species documented by thousands of researchers over many decades of work worldwide.
The goal of this research is to help researchers develop and use relatively simple tools to describe species in a way that makes those descriptions easier to share...
INDICATOR is a novel information system for collecting, integrating, and analyzing data from multiple sources to provide public health decision makers real-time data on the health of their community. Data comes from sources as varied as emergency department visits, school attendance, veterinary clinics, and social media postings and together have been used to change public policy in outbreak events.
Funding for this project was provided by the Carle Foundation, Centers for Disease Control and Prevention, and the U.S. Department of Agriculture.
Intelligent Medical Objects
National Science Foundation
This project will develop a mobile sensor technology for performing detection and identification of viral and bacterial pathogens. By means of a smartphone-based detection instrument, the results are shared with a cloud-based data management service that will enable physicians to rapidly visualize the geographical and temporal spread of infectious disease. When deployed by a community of medical users (such as veterinarians or point-of-care clinicians), the PathTracker system will enable rapid determination and reporting of instances of infectious disease that can inform treatment and quarantine responses that are currently not possible with tests performed at central laboratory facilities.
Immediate uses for the technology are for diagnosis of viral infection in human...
IN THE NEWS
The 2014 Ebola virus epidemic that originated in West Africa and spread to other parts of the globe was the deadliest Ebola outbreak in history. During this period, a frightened public turned to social media and internet search engines for information and to share news of the outbreak. According to a team of international researchers, including iSchool Research Scientist Ian Brooks, understanding the social media activity around a health crisis, like the 2014 Ebola outbreak, can help health organizations improve their communication strategies and prevent misinformation and panic.
Their paper, "Fear on the networks: analyzing the 2014 Ebola outbreak," was published in December in Pan American Journal of Public Health (41, 2017). In addition to Brooks, researchers included lead author Marcelo D’Agostino (Department of Communicable Diseases and...
Assistant Professor Jodi Schneider (MS ’08) has received funding from the National Institutes of Health to develop a series of automated informatics tools for reviewing medical literature more quickly and easily. The project, “Text Mining Pipeline to Accelerate Systematic Reviews in Evidence-Based Medicine,” was funded through a subaward from the University of Illinois at Chicago that will cover $228,006 in direct costs. Schneider is co-principal investigator with Neil Smalheiser, associate professor of psychiatry at UIC, and Aaron Cohen, a professor in the Oregon Health & Science University’s Department of Medical Informatics and Clinical Epidemiology.
The team is currently testing three informatics tools: a meta-search engine for finding articles in medical literatures across different databases; an automated randomized control trial (RCT) tagger for identifying human randomized controlled clinical trial articles; and an aggregator tool that clusters together RCT...
Associate Professor Catherine Blake has been named the iSchool's Centennial Scholar for 2017-2018. The award is endowed by alumni and friends of the School and given in recognition of outstanding accomplishments and/or professional promise in information sciences.
A leading researcher in text mining medical literature, Blake has returned from a year as a faculty fellow at the Lister Hill National Center for Biomedical Communications, a research and development unit of the National Library of Medicine at the National Institutes of Health (NIH). There she worked on projects in semantic knowledge representation and medical ontology research.
Blake's earlier focus on how people synthesize evidence from literature directly informs her computational approaches to accelerate scientific discovery. She utilizes her industrial experience as a software developer, formal training in information and computer science, and more than a decade of experience in text mining scientific...
Bruce Schatz is an affiliated faculty member at the iSchool.
Embedded in our society is a cultural memory of the old-time family doctor, a medical practitioner who knows of your family, your history, and your daily life, and uses that knowledge to provide the most optimal care. One Illinois faculty member and his research team have been working to move closer to that goal by exploiting a piece of familiar technology—the smartphone that can now be found in the average American's pocket.
Professor of Medical Information Science Bruce Schatz and coauthors previously developed software for Android phones that uses the phone's native motion sensor to predict a lung patient’s disease state. That prediction was based on the patient’s movements during an exam at a hospital. In a study published in Telemedicine and e-Health (DOI: 10.1089/tmj.2017.0008), the official journal of the...
A multidisciplinary group from the University of Illinois and the University of Washington at Tacoma (UW Tacoma) has developed a novel platform to diagnose infectious disease at the point of care, using a smartphone as the detection instrument in conjunction with a test kit in the format of a credit card. The group is led by Electrical and Computer Engineering Professor Brian T. Cunningham; iSchool Research Scientist Ian Brooks; Bioengineering Professor Rashid Bashir; Electrical and Computer Engineering Professor Steven Lumetta; and David L. Hirschberg, who is affiliated with UW Tacoma's School of Interdisciplinary Arts and Sciences. The team also includes iSchool MS student Smit Desai.
Assistant Professor Jodi Schneider will discuss her study of biomedical research reports at the 2nd European Conference on Argumentation, ECA Fribourg 2017, on June 20-23 in Fribourg, Switzerland. The theme of the conference is "Argumentation and Inference." She will also speak at the preconference, "Status, Relevance, and Authority of Facts."
Schneider and Sally Jackson, professor of communication at Illinois, are organizing "Innovations in Reasoning and Arguing about Health," a panel that will examine how the complex set of inference practices in the health care profession is changing as people discover better ways to arrive at conclusions about health.
"Inference, or steps in reasoning, is an important part of studying how we make decisions on any topic," said Schneider. "Everyone wants sound reasoning about health—patients, health care providers, public health institutions, medical researchers,...
Jodi Schneider (MS '08), assistant professor, is the recipient of a start-up allocation award from the Extreme Science and Engineering Discovery Environment (XSEDE). XSEDE is a project of the National Science Foundation that provides researchers with access to the world’s most advanced and powerful collection of integrated digital resources and services.
The award will support Schneider's research in biomedical informatics. The goal of her project is to make sense of large-scale networks of knowledge in biomedical literature. Her underlying code and data are provided by collaborators at the National Library of Medicine, who used text mining to process data from NLM's PubMed/MEDLINE to create a new database, SemMedDB.
"SemMedDB is a database with 'predications' like Drug X treats Disease Y. We consider this as a semantic network with drugs as vertices and relationships (e.g., treats) as edges. You can think of the...