New approach improves systematic reviews of scientific literature

Catherine Blake
Catherine Blake, Professor and MS/IM Program Director

Risk assessments are conducted to determine if a chemical found in the environment is harmful to public health; for example, answering questions such as "does chemical 'x' promote cancer?" Conducting an impartial analysis of chemicals is thus critical to ensure that public policies reflect the best available scientific evidence. Unfortunately, the process of retrieving, extracting, and analyzing findings reported in scientific literature is time consuming and can delay when policies are updated to reflect new evidence.

Professor Catherine Blake and Jodi A. Flaws, professor of comparative biosciences at the University of Illinois, have developed an automated approach that moves beyond the retrieval of relevant literature to the extraction step of the information synthesis process. In a recent study of cell death and proliferation—two fundamental hallmarks of cancer—they demonstrate how simply counting the number of outcomes shows a very different picture than focusing on how key outcomes have changed.

"Systems currently just focus on the retrieval step, and if you base decisions solely on the number of abstracts retrieved, you would make the wrong decision," said Blake. "You have to look at the directionality of the evidence."

The natural language processing (NLP) system that Blake developed scales to over 400,000 abstracts and identifies the directionality of evidence (refuting, neutral, or supporting) for 27 different chemicals. Their approach automates the extraction step, providing researchers with waffle plots that visually present the distribution of supporting, neutral, and refuting evidence for each chemical. For example, in the waffle plots below, chemical 1 has more refuting evidence whereas chemical 22 has more supporting evidence.

waffle plots of 27 chemicals showing refuting and supporting evidence

This automated approach provides researchers with important detail that is missing in existing automated systems, which is closer to the manual processes used in decision-making, and also maintains the level of transparency needed in a public policy setting. Blake and Flaws' study, "Using semantics to scale up evidence-based chemical risk-assessments," was recently published in the peer-reviewed open access journal PLOS One.

Blake's research seeks to accelerate science and inform policy by automatically extracting and summarizing claims reported in the scientific literature. She holds a PhD and MS in information and computer science from the University of California, Irvine, and an MS and BS in computer science from the University of Wollongong, Australia.

Updated on
Backto the news archive

Related News

New project to create accessible library makerspaces

Library makerspaces offer community members the opportunity to tinker, design, experiment, and create with a range of technology in an informal learning space. However, because current makerspaces and maker tools are highly vision oriented, blind and visually impaired (BVI) people have limited access to these learning opportunities. A new project led by Assistant Professor JooYoung Seo and Associate Professor Kyungwon Koh, director of the CU Community Fab Lab, seeks to address this problem by creating accessible maker programs for BVI learners and developing training materials for librarians and maker professionals on accessible making. The researchers were recently awarded a three-year $498,638 National Leadership grant from the Institute of Museum and Library Services (IMLS grant LG-252360-OLS-22) for their project, "Promoting Computational Thinking Skills for Blind and Visually Impaired Teens Through Accessible Library Makerspaces."

New role for Rusch

The iSchool is pleased to announce the appointment of Adam Rusch as a teaching assistant professor. He was most recently employed as an eLearning specialist in the College of Education, where he helped the college shift to emergency remote learning during the coronavirus pandemic and become one of the first units on the Urbana campus to completely transition to the Canvas Learning Management System.

Adam Rusch

New project to explore the use of conversational AI in libraries

Assistant Professor Yun Huang has been awarded a three-year $399,996 Early Career Development grant from the Institute of Museum and Library Services (IMLS grant RE-252329-OLS-22), under the Laura Bush 21st Century Librarian Program, which supports innovative research by untenured, tenure-track faculty.

Yun Huang

Knox elected chair of NCAC Board

The National Coalition Against Censorship (NCAC), an alliance of 59 national nonprofit organizations that is committed to the non-partisan defense of free expression, has elected Associate Professor Emily Knox as chair of its Board of Directors.

Emily Knox