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

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

Spectrum Scholar Spotlight: Zhaneille Green

Thirteen iSchool master's students were named 2022-2023 Spectrum Scholars by the American Library Association (ALA) Office for Diversity, Literacy, and Outreach Services. This "Spectrum Scholar Spotlight" series highlights the School's scholars. Zhaneille Green holds a BA in geography and history from Clark University in Worcester, Massachusetts.

Zhaneille Green

Digital age creates challenges for public libraries in providing patron privacy

Library professionals have long held sacred the right of patrons to privacy while using library facilities, and the privilege is explicitly addressed in the American Library Association's Bill of Rights. The advent of the digital age, however, has complicated libraries' efforts to secure and protect privacy, Associate Professor Masooda Bashir has learned.

Masooda Bashir

Student award recipients announced

Each year, the School of Information Sciences recognizes a group of outstanding students for their achievement in academics as well as a number of attributes that contribute to professional success. Congratulations to this year's honorees!

Ly Dinh and Jessica Cheng

Schneider named ACM Senior Member

Associate Professor Jodi Schneider has been named a Senior Member of the Association for Computing Machinery (ACM), the world's largest educational and scientific computing society. Senior Member status is bestowed on ACM members with at least ten years of professional experience and five years of professional membership who have demonstrated performance through technical leadership and technical or professional contributions. Schneider is one of 35 new Senior Members this quarter.

Jodi Schneider

New computational tools to protect Homeland Security data

Associate Professor Jingrui He is developing computational tools to protect against leaks and/or unauthorized use of sensitive data held and distributed among Department of Homeland Security (DHS) agencies and other parties. Her project, "Privacy-Preserving Analytics for Non-IID Data," has been awarded a three-year, $651,927 grant from the DHS Center for Accelerating Operational Efficiency (CAOE).

Jingrui He