NSF grant to accelerate synthetic biology discoveries

Stephen Downie
J. Stephen Downie, Professor, Associate Dean for Research, and Co-Director of the HathiTrust Research Center
Jacob Jett
Jacob Jett, Postdoctoral Research Associate

A multi-institutional $1.2M grant from the National Science Foundation will accelerate discovery and exploration of the synthetic biology design space. Professor and Associate Dean for Research J. Stephen Downie serves as a principal investigator on the project, "Synthetic Biology Knowledge Systems," which brings together researchers from the University of Illinois; University of Utah; University of California, San Diego; Virginia Commonwealth University; Worcester Polytechnic Institute; and the non-partisan and objective research organization NORC at the University of Chicago.

During the course of the two-year project, a multidisciplinary team of biological engineers, machine learning experts, data scientists, library scientists, and social scientists will build a knowledge system integrating disparate data and publication repositories. The goal will be to deliver effective and efficient information access to researchers who are currently using a trial-and-error approach because reliable information about prior experiments does not exist.

According to Postdoctoral Research Associate Jacob Jett, a lead researcher on the project, machine learning methods like named entity recognition, topic modeling, and word embeddings will be used to mine information from the existing synthetic biology literature.

"The results of these machine learning processes will be reconciled and grounded using existing knowledge representations of real-world entities like organisms, genes, proteins, and cell parts through ontologies and controlled vocabularies like the Gene Ontology, the Sequence Ontology, and the National Center for Biotechnology Information's organism taxonomy, among other vocabulary resources," Jett said.

The Illinois team will help build an information retrieval recommender system for the scientists and advise on the ontologies and metadata.

"Synthetic biology has a transformative potential in applications from energy, agriculture, materials, and health. Our participation in this important project illustrates how the iSchool can make unique contributions to harnessing the data revolution," Downie said.

Downie is codirector of the HathiTrust Research Center (HTRC), a collaboration between the University of Illinois, Indiana University, and the HathiTrust to enable advanced computational access to text found in the HathiTrust Digital Library. His research areas include the design and evaluation of information retrieval systems, including multimedia music information retrieval; the political economy of internetworked communication systems; database design; and Web-based technologies. He holds a bachelor’s degree in music theory and composition, along with master's and doctoral degrees in library and information science, all from the University of Western Ontario.

Jett's research is primarily focused on information modeling issues with a special focus on ontology, controlled vocabulary, and schema development for Semantic Web infrastructure. He uses a combination of formal conceptual analysis approaches to analyze and organize digital information systems such as databases, repositories, and digital libraries. Jett earned his PhD in library and information science from the iSchool at Illinois, where he also completed his master's and Certificate of Advanced Study work.

Updated on
Backto the news archive

Related News

Schwebel edits book on Newbery Medal books

Sara L. Schwebel, professor and director of The Center for Children's Books, and Jocelyn Van Tuyl, professor of French at New College of Florida, have coedited a new book, Dust Off the Gold Medal: Rediscovering Children's Literature at the Newbery Centennial, which was recently published by Routledge. The Newbery Medal, the oldest and most influential children's book award in the United States, marks its 100th anniversary this year. In Dust Off the Gold Medal, Schwebel and Van Tuyl collect fourteen essays, written by contributors across the country, who examine Newbery winners that have been understudied by literary scholars.

Sara Schwebel

Multi-institutional team receives NSF grant to fight online disinformation

The iSchool at Illinois is part of a multidisciplinary research team that has been awarded $750,000 to develop digital literacy tools to curb the deleterious effects of online disinformation. The grant is from the National Science Foundation's Convergence Accelerator, a program launched in 2019 that builds upon basic research and discovery to accelerate solutions toward societal impact. The research team, led by the University of Buffalo (UB), includes experts in artificial intelligence, the humanities, information science and other fields. In addition to Illinois and UB, partners include Clemson University, Lehigh University, and Northeastern University.

iSchool to host JCDL 2021

The iSchool at Illinois will host the 2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL), which will be held virtually from September 27-30. JCDL is a major international forum focusing on digital libraries and associated technical, practical, and social issues. The conference will feature paper and poster presentations as well as a wide variety of tutorials and workshops offering hands-on experiences with different digital libraries and online archives.

JCDL logo 2021

iSchool faculty ranked as excellent

Forty-seven iSchool instructors were named in the University's List of Teachers Ranked as Excellent for Spring 2021. The rankings are released every semester, and results are based on the Instructor and Course Evaluation System (ICES) questionnaire forms maintained by Measurement and Evaluation in the Center for Innovation in Teaching and Learning. Only those instructors who gave out ICES forms during the semester and who released their data for publication are included in the list.

iSchool Building

Join the iSchool at ALISE 2021

Join iSchool faculty, staff, and students for the annual conference of the Association for Library and Information Science Education (ALISE), which will take place virtually from September 20-24. The theme of ALISE 2021 is "Crafting a Resilient Future: Leadership, Education, and Inspiration."