New approach improves systematic reviews of scientific literature

Catherine Blake
Catherine Blake, Professor and Associate Dean for Academic Affairs

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

iSchool represented at Charleston Conference

iSchool adjunct and affiliate faculty will participate in virtual and in-person sessions of the 2024 Charleston Conference. The conference is an annual gathering that draws librarians, publishers, vendors, and others to discuss issues relating to the acquisition and publication of books and serials. 

Schneider group to present at ASIS&T workshop

Members of Associate Professor Jodi Schneider’s group will present their research at the Association for Information Science and Technology (ASIS&T) Workshop on Informetric, Scientometric, and Scientific and Technical Information Research, which will be held virtually on November 6 and 13. The MET-STI 2024 Workshop is collaboratively hosted by the Special Interest Group for Metrics (SIG-MET) and Special Interest Group for Scientific and Technical Information (SIG-STI) of ASIS&T.

Jodi Schneider

Wong co-edits new edition of Reference and Information Services

Adjunct Lecturer Melissa Wong (MSLIS '94) and Laura Saunders, professor of library and information science at Simmons University, are the co-editors of Reference and Information Services: An Introduction, Seventh Edition, which was recently published by Bloomsbury Libraries Unlimited. The textbook provides a comprehensive update to the previous edition, also co-edited by Wong and Saunders, and serves as an essential resource for LIS students and practitioners alike.

Melissa Wong

iSchool researchers to present at ASSETS 2024

iSchool faculty and students will present their research at the 26th International Association for Computing Machinery (ACM) Special Interest Group (SIG) ACCESS Conference on Computers and Accessibility (ASSETS 2024), which will be held on October 28-30 in St. John's, Newfoundland and Labrador, Canada. The conference is the premier forum for presenting research on design, evaluation, use, and education related to computing for people with disabilities and older adults.

iSchool well represented at ASIS&T 2024

iSchool faculty, staff, and students will participate in the 87th Annual Meeting of the Association for Information Science and Technology (ASIS&T), which will be held on October 25-29 in Calgary, Canada. The theme of this year's conference is "Putting People First: Responsibility, Reciprocity, and Care in Information Research and Practice." The meeting is the premier international conference dedicated to the study of information, people, and technology in contemporary society.

iSchool Building